1
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Wang S, Yang R, Song M, Li J, Zhou Y, Dai C, Song T. Current understanding of the role of DDX21 in orchestrating gene expression in health and diseases. Life Sci 2024; 349:122716. [PMID: 38762067 DOI: 10.1016/j.lfs.2024.122716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/30/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
RNA helicases are involved in almost all biological events, and the DDXs family is one of the largest subfamilies of RNA helicases. Recently, studies have reported that RNA helicase DDX21 is involved in several biological events, specifically in orchestrating gene expression. Hence, in this review, we provide a comprehensive overview of the function of DDX21 in health and diseases. In the genome, DDX21 contributes to genome stability by promoting DNA damage repair and resolving R-loops. It also facilitates transcriptional regulation by directly binding to promoter regions, interacting with transcription factors, and enhancing transcription through non-coding RNA. Moreover, DDX21 is involved in various RNA metabolism such as RNA processing, translation, and decay. Interestingly, the activity and function of DDX21 are regulated by post-translational modifications, which affect the localization and degradation of DDX21. Except for its role of RNA helicase, DDX21 also acts as a non-enzymatic function in unwinding RNA, regulating transcriptional modifications and promoting transcription. Next, we discuss the potential application of DDX21 as a clinical predictor for diseases, which may facilitate providing novel pharmacological targets for molecular therapy.
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Affiliation(s)
- Shaoshuai Wang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqi Yang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengzhen Song
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia Li
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; City of Hope Medical Center, Duarte, CA 91010, USA; Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Yanrong Zhou
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chen Dai
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan 430030, China.
| | - Tongxing Song
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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2
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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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3
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Andregic N, Weaver C, Basu S. The binding of a c-MYC promoter G-quadruplex to neurotransmitters: An analysis of G-quadruplex stabilization using DNA melting, fluorescence spectroscopy, surface-enhanced Raman scattering and molecular docking. Biochim Biophys Acta Gen Subj 2023; 1867:130473. [PMID: 37778448 DOI: 10.1016/j.bbagen.2023.130473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The interactions of several neurotransmitter and neural hormone molecules with the c-MYC G-quadruplex DNA sequence were analyzed using a combination of spectroscopic and computational techniques. The interactions between indole, catecholamine, and amino acid neurotransmitters and DNA sequences could potentially add to the understanding of the role of G-quadruplex structures play in various diseases. Also, the interaction of the DNA sequence derived from the nuclear hypersensitivity element (NHE) III1 region of c-MYC oncogene (Pu22), 5'-TGAGGGTGGGTAGGGTGGGTAA-3', has added significance in that these molecules may promote or inhibit the formation of G-quadruplex DNA which could lead to the development of promising drugs for anticancer therapy. The results showed that these molecules did not disrupt G-quadruplex formation even in the absence of quadruplex-stabilizing cations. There was also evidence of concentration-dependent binding and high binding affinities based on the Stern-Volmer model, and thermodynamically favorable interactions in the form of hydrogen-bonding and interactions involving the π system of the aromatic neurotransmitters.
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Affiliation(s)
- Nicole Andregic
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Caitlin Weaver
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Swarna Basu
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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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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Chatain J, Hatem G, Delagoutte E, Riou JF, Alberti P, Saintomé C. Multiple hPOT1-TPP1 cooperatively unfold contiguous telomeric G-quadruplexes proceeding from 3' toward 5', a feature due to a 3'-end binding preference and to structuring of telomeric DNA. Nucleic Acids Res 2021; 49:10735-10746. [PMID: 34534331 PMCID: PMC8501996 DOI: 10.1093/nar/gkab768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/04/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Telomeres are DNA repeated sequences that associate with shelterin proteins and protect the ends of eukaryotic chromosomes. Human telomeres are composed of 5'TTAGGG repeats and ends with a 3' single-stranded tail, called G-overhang, that can be specifically bound by the shelterin protein hPOT1 (human Protection of Telomeres 1). In vitro studies have shown that the telomeric G-strand can fold into stable contiguous G-quadruplexes (G4). In the present study we investigated how hPOT1, in complex with its shelterin partner TPP1, binds to telomeric sequences structured into contiguous G4 in potassium solutions. We observed that binding of multiple hPOT1-TPP1 preferentially proceeds from 3' toward 5'. We explain this directionality in terms of two factors: (i) the preference of hPOT1-TPP1 for the binding site situated at the 3' end of a telomeric sequence and (ii) the cooperative binding displayed by hPOT1-TPP1 in potassium. By comparing binding in K+ and in Li+, we demonstrate that this cooperative behaviour does not stem from protein-protein interactions, but from structuring of the telomeric DNA substrate into contiguous G4 in potassium. Our study suggests that POT1-TPP1, in physiological conditions, might preferentially cover the telomeric G-overhang starting from the 3'-end and proceeding toward 5'.
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Affiliation(s)
- Jean Chatain
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Georges Hatem
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Emmanuelle Delagoutte
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Jean-François Riou
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Carole Saintomé
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France.,Sorbonne Université, UFR927, F-75005 Paris, France
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6
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Chatain J, Blond A, Phan AT, Saintomé C, Alberti P. GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres. Nucleic Acids Res 2021; 49:7588-7601. [PMID: 34214172 PMCID: PMC8287962 DOI: 10.1093/nar/gkab518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson-Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.
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Affiliation(s)
- Jean Chatain
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
| | - Alain Blond
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d’Histoire naturelle, CNRS, Paris 75005, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Carole Saintomé
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
- Sorbonne Université, UFR927, Paris 75005, France
| | - Patrizia Alberti
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
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7
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Carrino S, Hennecker CD, Murrieta AC, Mittermaier A. Frustrated folding of guanine quadruplexes in telomeric DNA. Nucleic Acids Res 2021; 49:3063-3076. [PMID: 33693924 PMCID: PMC8034632 DOI: 10.1093/nar/gkab140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/22/2021] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Human chromosomes terminate in long, single-stranded, DNA overhangs of the repetitive sequence (TTAGGG)n. Sets of four adjacent TTAGGG repeats can fold into guanine quadruplexes (GQ), four-stranded structures that are implicated in telomere maintenance and cell immortalization and are targets in cancer therapy. Isolated GQs have been studied in detail, however much less is known about folding in long repeat sequences. Such chains adopt an enormous number of configurations containing various arrangements of GQs and unfolded gaps, leading to a highly frustrated energy landscape. To better understand this phenomenon, we used mutagenesis, thermal melting, and global analysis to determine stability, kinetic, and cooperativity parameters for GQ folding within chains containing 8–12 TTAGGG repeats. We then used these parameters to simulate the folding of 32-repeat chains, more representative of intact telomeres. We found that a combination of folding frustration and negative cooperativity between adjacent GQs increases TTAGGG unfolding by up to 40-fold, providing an abundance of unfolded gaps that are potential binding sites for telomeric proteins. This effect was most pronounced at the chain termini, which could promote telomere extension by telomerase. We conclude that folding frustration is an important and largely overlooked factor controlling the structure of telomeric DNA.
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Affiliation(s)
- Simone Carrino
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Ana C Murrieta
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.,School of Engineering and Sciences, Instituto Tecnológico y de Estudios Superiores De Monterrey, Av. Eugenio Garza Sada 2501 Sur Col. Tecnológico C.P. 64849, Monterrey, Nuevo León, México
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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8
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Monsen RC, Chakravarthy S, Dean WL, Chaires JB, Trent JO. The solution structures of higher-order human telomere G-quadruplex multimers. Nucleic Acids Res 2021; 49:1749-1768. [PMID: 33469644 PMCID: PMC7897503 DOI: 10.1093/nar/gkaa1285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/21/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Human telomeres contain the repeat DNA sequence 5′-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3′ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5′-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ∼34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, 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
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
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9
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Davletgildeeva AT, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Activity of Human Apurinic/Apyrimidinic Endonuclease APE1 Toward Damaged DNA and Native RNA With Non-canonical Structures. Front Cell Dev Biol 2020; 8:590848. [PMID: 33195255 PMCID: PMC7662432 DOI: 10.3389/fcell.2020.590848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
The primary role of apurinic/apyrimidinic (AP) endonuclease APE1 in human cells is the cleavage of the sugar phosphate backbone 5' to an AP site in DNA to produce a single-strand break with a 5'-deoxyribose phosphate and 3'-hydroxyl end groups. APE1 can also recognize and incise some damaged or modified nucleotides and possesses some minor activities: 3'-5' exonuclease, 3'-phosphodiesterase, 3'-phosphatase, and RNase H. A molecular explanation for the discrimination of structurally different substrates by the single active site of the enzyme remains elusive. Here, we report a mechanism of target nucleotide recognition by APE1 as revealed by the results of an analysis of the APE1 process involving damaged DNA and native RNA substrates with non-canonical structures. The mechanism responsible for substrate specificity proved to be directly related to the ability of a target nucleotide to get into the active site of APE1 in response to an enzyme-induced DNA distortion.
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Affiliation(s)
- Anastasia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
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10
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Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
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Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
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11
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Tu ATT, Hoshi K, Ikebukuro K, Hanagata N, Yamazaki T. Monomeric G-Quadruplex-Based CpG Oligodeoxynucleotides as Potent Toll-Like Receptor 9 Agonists. Biomacromolecules 2020; 21:3644-3657. [PMID: 32857497 DOI: 10.1021/acs.biomac.0c00679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic oligodeoxynucleotides (ODNs) containing unmethylated cytosine-phosphate-guanine (CpG) motifs trigger the immune response by stimulating endosomal Toll-like receptor (TLR) 9. Natural linear ODNs are susceptible to nuclease degradation, thereby limiting their clinical applications. Here, we designed monomeric G-quadruplex-based CpG ODNs (G4 CpG ODNs) containing CpG motifs in the central loop region of the G4 structure. The monomeric G4 CpG ODNs were more stable in serum than the linear ODNs. The monomeric G4 CpG ODNs containing two or three CpG motifs induced the production of immunostimulatory cytokines interleukin (IL)-6, IL-12, and interferon (IFN)-β in mouse macrophage-like RAW264 cells. We also showed that the number of CpG motifs and the number of nucleotides between the CpG motif and G-tracts define the efficacy of the G4 CpG ODNs in activating TLR9. Incubating human peripheral blood mononuclear cells with G4 CpG ODNs promoted IL-6 and IFN-γ production, confirming their stimulatory effects on human immune cells. Mice given intraperitoneal injections of G4 CpG ODNs produced higher plasma IL-6 compared with injections of linear ODNs. These findings provide further understanding of the parameters governing the immunostimulatory activity of G4 CpG ODNs, thereby providing insights into the rational design of highly potent G4 CpG ODNs for vaccine adjuvants.
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Affiliation(s)
- Anh Thi Tram Tu
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan.,Nanomedicine Group, Research Center for Functional Materials (RCFM), National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Kazuaki Hoshi
- Nanomedicine Group, Research Center for Functional Materials (RCFM), National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan
| | - Nobutaka Hanagata
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan.,Nanotechnology Innovation Station, National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Tomohiko Yamazaki
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan.,Nanomedicine Group, Research Center for Functional Materials (RCFM), National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
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12
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Ferino A, Nicoletto G, D'Este F, Zorzet S, Lago S, Richter SN, Tikhomirov A, Shchekotikhin A, Xodo LE. Photodynamic Therapy for ras-Driven Cancers: Targeting G-Quadruplex RNA Structures with Bifunctional Alkyl-Modified Porphyrins. J Med Chem 2020; 63:1245-1260. [PMID: 31930916 DOI: 10.1021/acs.jmedchem.9b01577] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Designing small molecules able to break down G4 structures in mRNA (RG4s) offers an interesting approach to cancer therapy. Here, we have studied cationic porphyrins (CPs) bearing an alkyl chain up to 12 carbons, as they bind to RG4s while generating reactive oxygen species upon photoirradiation. Fluorescence-activated cell sorting (FACS) and confocal microscopy showed that the designed alkyl CPs strongly penetrate cell membranes, binding to KRAS and NRAS mRNAs under low-abundance cell conditions. In Panc-1 cells, alkyl CPs at nanomolar concentrations promote a dramatic downregulation of KRAS and NRAS expression, but only if photoactivated. Alkyl CPs also reduce the metabolic activity of pancreatic cancer cells and the growth of a Panc-1 xenograft in SCID mice. Propidium iodide/annexin assays and caspase 3, caspase 7, and PARP-1 analyses show that these compounds activate apoptosis. All these data demonstrate that the designed alkyl CPs are efficient photosensitizers for the photodynamic therapy of ras-driven cancers.
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Affiliation(s)
- Annalisa Ferino
- Department of Medicine, Laboratory of Biochemistry , Univeristy of Udine , P.le Kolbe 4 , 33100 Udine , Italy
| | - Giulia Nicoletto
- Department of Medicine, Laboratory of Biochemistry , Univeristy of Udine , P.le Kolbe 4 , 33100 Udine , Italy
| | - Francesca D'Este
- Department of Medicine, Laboratory of Biochemistry , Univeristy of Udine , P.le Kolbe 4 , 33100 Udine , Italy
| | - Sonia Zorzet
- Department of Life Science , University of Trieste , P.le Europa 1 , 34127 Trieste , Italy
| | - Sara Lago
- Department of Molecular Medicine , University of Padova , via A. Gabelli 63 , 35121 Padova , Italy
| | - Sara N Richter
- Department of Molecular Medicine , University of Padova , via A. Gabelli 63 , 35121 Padova , Italy
| | - Alexander Tikhomirov
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , 119021 Moscow , Russia
| | - Andrey Shchekotikhin
- Gause Institute of New Antibiotics , B. Pirogovskaya 11 , 119021 Moscow , Russia
| | - Luigi E Xodo
- Department of Medicine, Laboratory of Biochemistry , Univeristy of Udine , P.le Kolbe 4 , 33100 Udine , Italy
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13
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Zhou K, Liu J, Xiong X, Cheng M, Hu X, Narva S, Zhao X, Wu Y, Zhang W. Design, synthesis of 4,5-diazafluorene derivatives and their anticancer activity via targeting telomeric DNA G-quadruplex. Eur J Med Chem 2019; 178:484-499. [PMID: 31202994 DOI: 10.1016/j.ejmech.2019.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 01/19/2023]
Abstract
In our work, 19 novel 4,5-diazafluorene derivatives (11a-d, 12a-d, 13a-d, 14a-c, 15c, 16a-c) bearing a 1,3-disubstituted pyrazol/thioxothiazolidinone or thioxothiazolidinone-oxadiazole moieties were designed, synthesized, preliminarily explored for their antitumor activities and in vitro mechanism. All compounds showed different values of antiproliferative activity against A549, AGS, HepG2 and MCF-7 cell lines through CCK-8. Especially, the compound 14c exhibited the strongest activity and best selectivity against A549 cells with an IC50 1.13 μM and an SI value of 7.01 relative to MRC-5 cells, which was better than cisplatin (SI = 1.80) as a positive control. Experimental results at extracellular level demonstrated that compounds 14a-c could strongly interact with the G-quadruplex(es) formed in a 26 nt telomeric G-rich DNA, in particular, the 14c exhibits quite strong binding affinity with an association equilibrium constant (KA) of 7.04(±0.16) × 107 M-1 and more than 1000-fold specificity to G4-DNA over ds-DNA and Mut-DNA at the compound/G4-DNA ratio of 1:1. Further trap assay ascertained that compounds 14a-c owned strong inhibitory ability of telomerase activity in A549 cells, suggesting that these compounds have great possibility to target telomeric G-quadruplexes and consequently indirectly inhibit the telomerase activity. In addition, it is worthy of note that the remarkable inhibitory effects of 14a-c on the mobility of tested cancer cells were observed by wound healing assays. Furthermore, molecular docking and UV-Vis spectral results unclose the rationale for the interaction of compounds with such G-quadruplex(es). These results indicate that the growth and metastasis inhibition of cancer cells mediated by these 4,5-diazafluorene derivatives possibly result from their interaction with telomeric G-quadruplexes, suggesting that 4,5-diazafluorene derivatives, especially 14c, possess potential as anticancer drugs.
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Affiliation(s)
- Kang Zhou
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiachun Liu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xuqiong Xiong
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mei Cheng
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaolin Hu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Suresh Narva
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoyin Zhao
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China.
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14
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Fleming AM, Stewart KM, Eyring GM, Ball TE, Burrows CJ. Unraveling the 4n - 1 rule for DNA i-motif stability: base pairs vs. loop lengths. Org Biomol Chem 2019; 16:4537-4546. [PMID: 29873385 DOI: 10.1039/c8ob01198b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Previously our laboratory identified that poly-2'-deoxycytidine (dCn) strands of DNA with lengths greater than 12 nucleotides could adopt i-motif folds, while the pH-dependent stabilities follow a 4n - 1 repeat pattern with respect to chain length (J. Am. Chem. Soc., 2017, 139, 4682-4689). Herein, model i-motif folds in which loop configurations were forced by judiciously mutating dC to non-dC nucleotides allowed a structural model to be proposed to address this phenomenon. The model was developed by systematically studying two i-motifs with either an even or odd number of d(C·C)+ hemiprotonated base pairs in the core. First, a trend in the pH-dependent stability vs. loop nucleotide identity was observed: dC > dT ∼ dU ≫ dA ∼ dG. Next, loops comprised of dT nucleotides in the two different core base pair configurations were studied while systematically changing the loop lengths. We found that an i-motif with an even number of base pairs in the core with a single nucleotide in each of the three loops was the most stable, as well as an i-motif with an odd number of core base pairs having one nucleotide in the two exterior loops and three nucleotides in the central loop. A systematic increase in the central loop from 1-4 nucleotides for an odd number of base pairs in the i-motif core reproduced the 4n - 1 repeat pattern observed in the poly-dCn strands. Additional loop configurations were studied to further support the model. The results are discussed with respect to their biological relevance.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, 315 S. 1400 East. and University of Utah, Salt Lake City, UT 84112-0850, USA.
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15
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Hwang IP, Mailliet P, Hossard V, Riou JF, Bugaut A, Roger L. Investigating the Effect of Mono- and Dimeric 360A G-Quadruplex Ligands on Telomere Stability by Single Telomere Length Analysis (STELA). Molecules 2019; 24:molecules24030577. [PMID: 30736276 PMCID: PMC6384687 DOI: 10.3390/molecules24030577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 11/16/2022] Open
Abstract
Telomeres are nucleoprotein structures that cap and protect the natural ends of chromosomes. Telomeric DNA G-rich strands can form G-quadruplex (or G4) structures. Ligands that bind to and stabilize G4 structures can lead to telomere dysfunctions by displacing shelterin proteins and/or by interfering with the replication of telomeres. We previously reported that two pyridine dicarboxamide G4 ligands, 360A and its dimeric analogue (360A)2A, were able to displace in vitro hRPA (a single-stranded DNA-binding protein of the replication machinery) from telomeric DNA by stabilizing the G4 structures. In this paper, we perform for the first time single telomere length analysis (STELA) to investigate the effect of G4 ligands on telomere length and stability. We used the unique ability of STELA to reveal the full spectrum of telomere lengths at a chromosome terminus in cancer cells treated with 360A and (360A)2A. Upon treatment with these ligands, we readily detected an increase of ultrashort telomeres, whose lengths are significantly shorter than the mean telomere length, and that could not have been detected by other methods.
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Affiliation(s)
- In Pyo Hwang
- "Structure and Instability of Genomes" Laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 43 rue Cuvier, 75005 Paris, France.
| | - Patrick Mailliet
- "Structure and Instability of Genomes" Laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 43 rue Cuvier, 75005 Paris, France.
| | - Virginie Hossard
- "Structure and Instability of Genomes" Laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 43 rue Cuvier, 75005 Paris, France.
| | - Jean-Francois Riou
- "Structure and Instability of Genomes" Laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 43 rue Cuvier, 75005 Paris, France.
| | - Anthony Bugaut
- "Structure and Instability of Genomes" Laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 43 rue Cuvier, 75005 Paris, France.
| | - Lauréline Roger
- "Structure and Instability of Genomes" Laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 43 rue Cuvier, 75005 Paris, France.
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16
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Bielskutė S, Plavec J, Podbevšek P. Impact of Oxidative Lesions on the Human Telomeric G-Quadruplex. J Am Chem Soc 2019; 141:2594-2603. [PMID: 30657306 PMCID: PMC6727377 DOI: 10.1021/jacs.8b12748] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Telomere
attrition is closely associated with cell aging and exposure
to reactive oxygen species (ROS). While oxidation products of nucleotides
have been studied extensively in the past, the underlying secondary/tertiary
structural changes in DNA remain poorly understood. In this work,
we systematically probed guanine positions in the human telomeric
oligonucleotide sequence (hTel) by substitutions with the major product
of ROS, 8-oxo-7,8-dihydroguanine (oxoG), and evaluated
the G-quadruplex forming ability of such oligonucleotides. Due to
reduced hydrogen-bonding capability caused by oxoG, a loss
of G-quadruplex structure was observed for most oligonucleotides containing
oxidative lesions. However, some positions in the hTel sequence were
found to tolerate substitutions with oxoG. Due to oxoG’s preference for the syn conformation, distinct responses were observed when replacing guanines
with different glycosidic conformations. Accommodation of oxoG at sites originally in syn or anti in nonsubstituted hTel G-quadruplex requires a minor structural
rearrangement or a major conformational shift, respectively. The system
responds by retaining or switching to a fold where oxoG
is in syn conformation. Most importantly, these G-quadruplex
structures are still stable at physiological temperatures and should
be considered detrimental in higher-order telomere structures.
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Affiliation(s)
- Stasė Bielskutė
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Janez Plavec
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia
| | - Peter Podbevšek
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia
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17
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Burra S, Marasco D, Malfatti MC, Antoniali G, Virgilio A, Esposito V, Demple B, Galeone A, Tell G. Human AP-endonuclease (Ape1) activity on telomeric G4 structures is modulated by acetylatable lysine residues in the N-terminal sequence. DNA Repair (Amst) 2018; 73:129-143. [PMID: 30509560 DOI: 10.1016/j.dnarep.2018.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 02/08/2023]
Abstract
Loss of telomeres stability is a hallmark of cancer cells. Exposed telomeres are prone to aberrant end-joining reactions leading to chromosomal fusions and translocations. Human telomeres contain repeated TTAGGG elements, in which the 3' exposed strand may adopt a G-quadruplex (G4) structure. The guanine-rich regions of telomeres are hotspots for oxidation forming 8-oxoguanine, a lesion that is handled by the base excision repair (BER) pathway. One key player of this pathway is Ape1, the main human endonuclease processing abasic sites. Recent evidences showed an important role for Ape1 in telomeric physiology, but the molecular details regulating Ape1 enzymatic activities on G4-telomeric sequences are lacking. Through a combination of in vitro assays, we demonstrate that Ape1 can bind and process different G4 structures and that this interaction involves specific acetylatable lysine residues (i.e. K27/31/32/35) present in the unstructured N-terminal sequence of the protein. The cleavage of an abasic site located in a G4 structure by Ape1 depends on the DNA conformation or the position of the lesion and on electrostatic interactions between the protein and the nucleic acids. Moreover, Ape1 mutants mimicking the acetylated protein display increased cleavage activity for abasic sites. We found that nucleophosmin (NPM1), which binds the N-terminal sequence of Ape1, plays a role in modulating telomere length and Ape1 activity at abasic G4 structures. Thus, the Ape1 N-terminal sequence is an important relay site for regulating the enzyme's activity on G4-telomeric sequences, and specific acetylatable lysine residues constitute key regulatory sites of Ape1 enzymatic activity dynamics at telomeres.
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Affiliation(s)
- Silvia Burra
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Bruce Demple
- Department of Pharmacological Sciences, Stony Brook University, School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Aldo Galeone
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy.
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18
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Varizhuk AM, Protopopova AD, Tsvetkov VB, Barinov NA, Podgorsky VV, Tankevich MV, Vlasenok MA, Severov VV, Smirnov IP, Dubrovin EV, Klinov DV, Pozmogova GE. Polymorphism of G4 associates: from stacks to wires via interlocks. Nucleic Acids Res 2018; 46:8978-8992. [PMID: 30107602 PMCID: PMC6158749 DOI: 10.1093/nar/gky729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 01/16/2023] Open
Abstract
We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intramolecular structures and/or interlocked dimers and trimers to wires. Decreasing the annealing rate and increasing salt or oligonucleotide concentrations shifted the equilibrium from intramolecular G4s to higher-order structures. Control antiparallel and hybrid G4s demonstrated no polymorphism or aggregation in our experiments. The modification that mimics abasic sites (1',2'-dideoxyribose residues) in loops enhanced the oligomerization/multimerization of both the 2-tetrad and 3-tetrad G4 motifs. Our results shed light on the rules that govern G4 rearrangements. Gaining control over G4 folding enables the harnessing of the full potential of such structures for guided assembly of supramolecular DNA structures for nanotechnology.
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Affiliation(s)
- Anna M Varizhuk
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Anna D Protopopova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Vladimir B Tsvetkov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Nikolay A Barinov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Victor V Podgorsky
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Maria V Tankevich
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Maria A Vlasenok
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Vyacheslav V Severov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Igor P Smirnov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Evgeniy V Dubrovin
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Dmitry V Klinov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Galina E Pozmogova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
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19
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Huang S, Liang Y, Cui J, Xie J, Liu Y, Hu B, Xiao Q. Comparative investigation of binding interactions with three steroidal derivatives of d(GGGT) 4 G-quadruplex aptamer. Steroids 2018; 132:46-55. [PMID: 29458054 DOI: 10.1016/j.steroids.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 11/19/2022]
Abstract
Steroidal derivatives have attracted tremendous attentions in biological and biomedical areas, due to their variety biological activities. The investigation of structural influences helps in understanding their biological activities. The interactions of steroidal derivatives with DNA may play important roles in biological activities, however only a few investigations were reported on this issue. Herein, the structural influences of three steroidal derivatives were investigated based on their binding interactions with d(GGGT)4 G-quadruplex aptamer by spectroscopic approaches, nuclear magnetic resonance (NMR), electrochemical methods, and molecular modeling techniques. Three compounds were found to selectively bind with parallel G-quadruplex aptamer to form three complexes through end-stacking binding modes. Three compounds stabilized the G-quadruplex structure of the aptamer at different levels, which enhanced the biological activity of this aptamer to some extent. The space steric hindrance was responsible for differences in the binding interactions between d(GGGT)4 G-quadruplex aptamer and three compounds. These results provide new information for the molecular understanding of binding interactions of steroidal derivatives with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Shan Huang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Yu Liang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Jianguo Cui
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China.
| | - Jiangning Xie
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Yi Liu
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Baoqing Hu
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Qi Xiao
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China.
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20
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Saintomé C, Alberti P, Guinot N, Lejault P, Chatain J, Mailliet P, Riou JF, Bugaut A. Binding properties of mono- and dimeric pyridine dicarboxamide ligands to human telomeric higher-order G-quadruplex structures. Chem Commun (Camb) 2018; 54:1897-1900. [PMID: 29393312 DOI: 10.1039/c7cc07048a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here, we report on the in vitro binding properties of the known pyridine dicarboxamide G-quadruplex ligand 360A and a new dimeric analogue (360A)2A to human telomeric DNA higher-order G-quadruplex (G4) structures. This study points to original binding features never reported for G4 ligands, and reveals a greater efficiency for the dimeric ligand to displace RPA (a ssDNA binding protein involved in telomere replication) from telomeric DNA.
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Affiliation(s)
- C Saintomé
- "Structure and Instability of Genomes" laboratory, Sorbonne Universités, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 75005 Paris, France.
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21
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Lancrey A, Safa L, Chatain J, Delagoutte E, Riou JF, Alberti P, Saintomé C. The binding efficiency of RPA to telomeric G-strands folded into contiguous G-quadruplexes is independent of the number of G4 units. Biochimie 2017; 146:68-72. [PMID: 29191792 DOI: 10.1016/j.biochi.2017.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022]
Abstract
Replication protein A (RPA) is a single-stranded DNA binding protein involved in replication and in telomere maintenance. During telomere replication, G-quadruplexes (G4) can accumulate on the lagging strand template and need to be resolved. It has been shown that human RPA is able to unfold a single G4. Nevertheless, the G-strand of human telomeres is prone to fold into higher-order structures formed by contiguous G-quadruplexes. To understand how RPA deals with these structures, we studied its interaction with telomeric G-strands folding into an increasing number of contiguous G4s. The aim of this study was to determine whether the efficiency of binding/unfolding of hRPA to telomeric G-strands depends on the number of G4 units. Our data show that the number n of contiguous G4 units (n ≥ 2) does not affect the efficiency of hRPA to coat transiently exposed single-stranded telomeric G-strands. This feature may be essential in preventing instability due to G4 structures during telomere replication.
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Affiliation(s)
- Astrid Lancrey
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France
| | - Layal Safa
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France
| | - Jean Chatain
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France
| | - Emmanuelle Delagoutte
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France
| | - Jean-François Riou
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France.
| | - Carole Saintomé
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UFR927, F-75005, Paris, France.
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Kumagai A, Dunphy WG. MTBP, the partner of Treslin, contains a novel DNA-binding domain that is essential for proper initiation of DNA replication. Mol Biol Cell 2017; 28:2998-3012. [PMID: 28877985 PMCID: PMC5662258 DOI: 10.1091/mbc.e17-07-0448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 01/24/2023] Open
Abstract
MTBP, the partner of Treslin, contains a novel DNA-binding domain that associates with double-stranded DNA and G-quadruplex DNA. Mutants of MTBP that lack a functional version of this domain cannot support normal initiation of DNA replication. Treslin, which is essential for incorporation of Cdc45 into the replicative helicase, possesses a partner called MTBP (Mdm2-binding protein). We have analyzed Xenopus and human MTBP to assess its role in DNA replication. Depletion of MTBP from Xenopus egg extracts, which also removes Treslin, abolishes DNA replication. These extracts be can rescued with recombinant Treslin-MTBP but not Treslin or MTBP alone. Thus, Treslin-MTBP is collectively necessary for replication. We have identified a C-terminal region of MTBP (the CTM domain) that binds efficiently to both double-stranded DNA and G-quadruplex (G4) DNA. This domain also exhibits homology with budding yeast Sld7. Mutants of MTBP without a functional CTM domain are defective for DNA replication in Xenopus egg extracts. These mutants display an impaired localization to chromatin and the inability to support loading of Cdc45. Human cells harboring such a mutant also display severe S-phase defects. Thus, the CTM domain of MTBP plays a critical role in localizing Treslin-MTBP to the replication apparatus for initiation.
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Affiliation(s)
- Akiko Kumagai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - William G Dunphy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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Sun XY, Zhao P, Jin SF, Liu MC, Wang XH, Huang YM, Cheng ZF, Yan SQ, Li YY, Chen YQ, Zhong YM. Shedding lights on the flexible-armed porphyrins: Human telomeric G4 DNA interaction and cell photocytotoxicity research. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 173:606-617. [DOI: 10.1016/j.jphotobiol.2017.06.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 01/21/2023]
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Liu J, Chen M, Wang Y, Zhao X, Wang S, Wu Y, Zhang W. Synthesis and the interaction of 2-(1 H -pyrazol-4-yl)-1 H -imidazo[4,5-f][1,10]phenanthrolines with telomeric DNA as lung cancer inhibitors. Eur J Med Chem 2017; 133:36-49. [DOI: 10.1016/j.ejmech.2017.03.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/04/2017] [Accepted: 03/15/2017] [Indexed: 01/16/2023]
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25
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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27
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Saintomé C, Amrane S, Mergny JL, Alberti P. The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium. Nucleic Acids Res 2016; 44:2926-35. [PMID: 26762980 PMCID: PMC4824101 DOI: 10.1093/nar/gkw003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/31/2015] [Indexed: 11/14/2022] Open
Abstract
DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)7GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45°C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium.
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Affiliation(s)
- Carole Saintomé
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum national d'Histoire naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France UPMC (Université Pierre et Marie Curie) Université Paris 6, UFR 927, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, Bordeaux, France IECB (Institut Européen de Chimie et Biologie), Inserm U 869, Pessac, France
| | - Jean-Louis Mergny
- Université de Bordeaux, ARNA Laboratory, Bordeaux, France IECB (Institut Européen de Chimie et Biologie), Inserm U 869, Pessac, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Sorbonne Universités, Muséum national d'Histoire naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France
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