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Lauria A, La Monica G, Terenzi A, Mannino G, Bonsignore R, Bono A, Almerico AM, Barone G, Gentile C, Martorana A. Antiproliferative Properties and G-Quadruplex-Binding of Symmetrical Naphtho[1,2-b:8,7-b']dithiophene Derivatives. Molecules 2021; 26:molecules26144309. [PMID: 34299583 PMCID: PMC8303715 DOI: 10.3390/molecules26144309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Background: G-quadruplex (G4) forming sequences are recurrent in telomeres and promoter regions of several protooncogenes. In normal cells, the transient arrangements of DNA in G-tetrads may regulate replication, transcription, and translation processes. Tumors are characterized by uncontrolled cell growth and tissue invasiveness and some of them are possibly mediated by gene expression involving G-quadruplexes. The stabilization of G-quadruplex sequences with small molecules is considered a promising strategy in anticancer targeted therapy. Methods: Molecular virtual screening allowed us identifying novel symmetric bifunctionalized naphtho[1,2-b:8,7-b’]dithiophene ligands as interesting candidates targeting h-Telo and c-MYC G-quadruplexes. A set of unexplored naphtho-dithiophene derivatives has been synthesized and biologically tested through in vitro antiproliferative assays and spectroscopic experiments in solution. Results: The analysis of biological and spectroscopic data highlighted noteworthy cytotoxic effects on HeLa cancer cell line (GI50 in the low μM range), but weak interactions with G-quadruplex c-MYC promoter. Conclusions: The new series of naphtho[1,2-b:8,7-b’]dithiophene derivatives, bearing the pharmacophoric assumptions necessary to stabilize G-quadruplexes, have been designed and successfully synthesized. The interesting antiproliferative results supported by computer aided rational approaches suggest that these studies are a significant starting point for a lead optimization process and the isolation of a more efficacious set of G-quadruplexes stabilizers.
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Affiliation(s)
- Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Gabriele La Monica
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Alessio Terenzi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/A, 10135 Turin, Italy;
| | - Riccardo Bonsignore
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany;
| | - Alessia Bono
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
- Correspondence: ; Tel.: +39-091-2389-6821
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G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target. J Bacteriol 2021; 203:e0057720. [PMID: 33649149 DOI: 10.1128/jb.00577-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA strands consisting of multiple runs of guanines can adopt a noncanonical, four-stranded DNA secondary structure known as G-quadruplex or G4 DNA. G4 DNA is thought to play an important role in transcriptional and translational regulation of genes, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. In other organisms, including several bacterial pathogens and some plant species, the biological roles of G4 DNA and G4 RNA are starting to be explored. Recent investigations showed that G4 DNA and G4 RNA are generally conserved across plant species. In silico analyses of several bacterial genomes identified putative guanine-rich, G4 DNA-forming sequences in promoter regions. The sequences were particularly abundant in certain gene classes, suggesting that these highly diverse structures can be employed to regulate the expression of genes involved in secondary metabolite synthesis and signal transduction. Furthermore, in the pathogen Mycobacterium tuberculosis, the distribution of G4 motifs and their potential role in the regulation of gene transcription advocate for the use of G4 ligands to develop novel antitubercular therapies. In this review, we discuss the various roles of G4 structures in bacterial DNA and the application of G4 DNA as inhibitors or therapeutic agents to address bacterial pathogens.
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53
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Wang Y, Li C, Hao X, Wang L, Ma X, Jin R, Kang C, Gao L. Hydrogen-bond-driven dimers of naphthyridine derivatives for selective identification of DNA G-quadruplexes. Org Biomol Chem 2021; 19:4768-4774. [PMID: 33978052 DOI: 10.1039/d1ob00651g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-quadruplex (GQ) ligands as potential anti-cancer drugs have received extensive attention. Large aromatic systems are usually considered in the design of the ligands to improve the binding with GQs, which are typically constructed by the combination of small modules with covalent bonds. In this study, we presented a non-covalent bond approach to construct GQ ligands with an extended planar structure. The ligands were stable dimers assembled through quadruplex intermolecular hydrogen bonds between two molecules of naphthyridine derivatives. Spectroscopic analyses showed that dimeric ligands could stabilize GQs with an increase of the melting temperature up to 12 °C and induced conformational conversion of hybrid GQs. Confocal fluorescence microscopy confirmed the enrichment of naphthyridine ligands in the nucleus. The ligands showed moderate cytotoxicity against HeLa cells with an IC50 value of 7.5 μg mL-1 and effectively induced growth inhibition and apoptosis in HeLa cells. These results confirmed the feasibility of the quick building of GQ ligands through intermolecular interactions of simple molecules that are easily obtained during synthesis, which is helpful for GQ ligand design and quick establishment of a ligand library through the self-assembly of easily available molecular components.
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Affiliation(s)
- Yu Wang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. and University of Science and Technology of China, Hefei 230026, China
| | - Chunjie Li
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Xueyu Hao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. and University of Science and Technology of China, Hefei 230026, China
| | - Liangpeng Wang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Xiaoye Ma
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Rizhe Jin
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Chuanqing Kang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. and University of Science and Technology of China, Hefei 230026, China
| | - Lianxun Gao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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Tassinari M, Richter SN, Gandellini P. Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome. Nucleic Acids Res 2021; 49:3617-3633. [PMID: 33721024 PMCID: PMC8053107 DOI: 10.1093/nar/gkab127] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Noncoding RNAs are functional transcripts that are not translated into proteins. They represent the largest portion of the human transcriptome and have been shown to regulate gene expression networks in both physiological and pathological cell conditions. Research in this field has made remarkable progress in the comprehension of how aberrations in noncoding RNA drive relevant disease-associated phenotypes; however, the biological role and mechanism of action of several noncoding RNAs still need full understanding. Besides fulfilling its function through sequence-based mechanisms, RNA can form complex secondary and tertiary structures which allow non-canonical interactions with proteins and/or other nucleic acids. In this context, the presence of G-quadruplexes in microRNAs and long noncoding RNAs is increasingly being reported. This evidence suggests a role for RNA G-quadruplexes in controlling microRNA biogenesis and mediating noncoding RNA interaction with biological partners, thus ultimately regulating gene expression. Here, we review the state of the art of G-quadruplexes in the noncoding transcriptome, with their structural and functional characterization. In light of the existence and further possible development of G-quadruplex binders that modulate G-quadruplex conformation and protein interactions, we also discuss the therapeutic potential of G-quadruplexes as targets to interfere with disease-associated noncoding RNAs.
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Affiliation(s)
- Martina Tassinari
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padova, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
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Guillon J, Denevault-Sabourin C, Chevret E, Brachet-Botineau M, Milano V, Guédin-Beaurepaire A, Moreau S, Ronga L, Savrimoutou S, Rubio S, Ferrer J, Lamarche J, Mergny JL, Viaud-Massuard MC, Ranz M, Largy E, Gabelica V, Rosu F, Gouilleux F, Desplat V. Design, synthesis, and antiproliferative effect of 2,9-bis[4-(pyridinylalkylaminomethyl)phenyl]-1,10-phenanthroline derivatives on human leukemic cells by targeting G-quadruplex. Arch Pharm (Weinheim) 2021; 354:e2000450. [PMID: 33852185 DOI: 10.1002/ardp.202000450] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 11/07/2022]
Abstract
Current multiagent chemotherapy regimens have improved the cure rate in acute leukemia patients, but they are highly toxic and poorly efficient in relapsed patients. To improve the treatment approaches, new specific molecules are needed. The G-quadruplexes (G4s), which are noncanonical nucleic acid structures found in specific guanine-rich DNA or RNA, are involved in many cellular events, including control of gene expression. G4s are considered as targets for the development of anticancer agents. Heterocyclic molecules are well known to target and stabilize G4 structures. Thus, a new series of 2,9-bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline derivatives (1a-i) was designed, synthesized, and evaluated against five human myeloid leukemia cell lines (K562, KU812, MV4-11, HL60, and U937). Their ability to stabilize various oncogene promoter G4 structures (c-MYC, BCL-2, and K-RAS) as well as the telomeric G4 was also determined through the fluorescence resonance energy transfer melting assay and native mass spectrometry. In addition, the more bioactive ligands 1g-i were tested for telomerase activity in HuT78 and MV4-11 protein extracts.
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Affiliation(s)
- Jean Guillon
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Caroline Denevault-Sabourin
- Groupe Innovation et Ciblage Cellulaire, UFR des Sciences Pharmaceutiques, Université Tours, EA GICC-ERL 7001 CNRS, Tours, France
| | - Edith Chevret
- Cutaneous Lymphoma Oncogenesis Team, Bordeaux Research in Translational Oncology (BaRITOn), Université Bordeaux, INSERM U1053, Bordeaux, France
| | - Marie Brachet-Botineau
- Groupe Innovation et Ciblage Cellulaire, UFR des Sciences Pharmaceutiques, Université Tours, EA GICC-ERL 7001 CNRS, Tours, France
- Service d'Hématologie Biologique, CHRU de Tours, Tours, France
| | - Vittoria Milano
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Aurore Guédin-Beaurepaire
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Stéphane Moreau
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Luisa Ronga
- Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS UMR 5254, IPREM, Pau, France
| | - Solène Savrimoutou
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Sandra Rubio
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
| | - Jacky Ferrer
- Cutaneous Lymphoma Oncogenesis Team, Bordeaux Research in Translational Oncology (BaRITOn), Université Bordeaux, INSERM U1053, Bordeaux, France
| | - Jeremy Lamarche
- Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS UMR 5254, IPREM, Pau, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, UFR des Sciences Pharmaceutiques, Bordeaux, France
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Marie-Claude Viaud-Massuard
- Groupe Innovation et Ciblage Cellulaire, UFR des Sciences Pharmaceutiques, Université Tours, EA GICC-ERL 7001 CNRS, Tours, France
| | - Matthieu Ranz
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, Pessac, France
| | - Eric Largy
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, Pessac, France
| | - Valérie Gabelica
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, Pessac, France
| | - Frédéric Rosu
- IECB (Institut Européen de Chimie et Biologie), Université Bordeaux, CNRS, INSERM, UMS 3033 US001, Pessac, France
| | | | - Vanessa Desplat
- Cellules souches hématopoïétiques normales et leucémiques, UFR des Sciences Pharmaceutiques, Université Bordeaux, INSERM, U1035, Bordeaux, France
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TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity. Sci Rep 2021; 11:3509. [PMID: 33568696 PMCID: PMC7876106 DOI: 10.1038/s41598-021-82406-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Abstract
Telomere dysfunction causes chromosomal instability which is associated with many cancers and age-related diseases. The non-coding telomeric repeat-containing RNA (TERRA) forms a structural and regulatory component of the telomere that is implicated in telomere maintenance and chromosomal end protection. The basic N-terminal Gly/Arg-rich (GAR) domain of telomeric repeat-binding factor 2 (TRF2) can bind TERRA but the structural basis and significance of this interaction remains poorly understood. Here, we show that TRF2 GAR recognizes G-quadruplex features of TERRA. We show that small molecules that disrupt the TERRA-TRF2 GAR complex, such as N-methyl mesoporphyrin IX (NMM) or genetic deletion of TRF2 GAR domain, result in the loss of TERRA, and the induction of γH2AX-associated telomeric DNA damage associated with decreased telomere length, and increased telomere aberrations, including telomere fragility. Taken together, our data indicates that the G-quadruplex structure of TERRA is an important recognition element for TRF2 GAR domain and this interaction between TRF2 GAR and TERRA is essential to maintain telomere stability.
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Savva L, Georgiades SN. Recent Developments in Small-Molecule Ligands of Medicinal Relevance for Harnessing the Anticancer Potential of G-Quadruplexes. Molecules 2021; 26:molecules26040841. [PMID: 33562720 PMCID: PMC7914483 DOI: 10.3390/molecules26040841] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes, a family of tetraplex helical nucleic acid topologies, have emerged in recent years as novel targets, with untapped potential for anticancer research. Their potential stems from the fact that G-quadruplexes occur in functionally-important regions of the human genome, such as the telomere tandem sequences, several proto-oncogene promoters, other regulatory regions and sequences of DNA (e.g., rDNA), as well as in mRNAs encoding for proteins with roles in tumorigenesis. Modulation of G-quadruplexes, via interaction with high-affinity ligands, leads to their stabilization, with numerous observed anticancer effects. Despite the fact that only a few lead compounds for G-quadruplex modulation have progressed to clinical trials so far, recent advancements in the field now create conditions that foster further development of drug candidates. This review highlights biological processes through which G-quadruplexes can exert their anticancer effects and describes, via selected case studies, progress of the last few years on the development of efficient and drug-like G-quadruplex-targeted ligands, intended to harness the anticancer potential offered by G-quadruplexes. The review finally provides a critical discussion of perceived challenges and limitations that have previously hampered the progression of G-quadruplex-targeted lead compounds to clinical trials, concluding with an optimistic future outlook.
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Kumari N, Raghavan SC. G-quadruplex DNA structures and their relevance in radioprotection. Biochim Biophys Acta Gen Subj 2021; 1865:129857. [PMID: 33508382 DOI: 10.1016/j.bbagen.2021.129857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND DNA, the genetic material of most of the organisms, is the crucial element of life. Integrity of DNA needs to be maintained for transmission of genetic material from one generation to another. All organisms are constantly challenged by the environmental conditions which can lead to the induction of DNA damage. Ionizing radiation (IR) has been known to induce DNA damage and IR sensitivity varies among different organisms. The causes for differential radiosensitivity among various organisms have not been studied in great detail. SCOPE OF REVIEW We discuss DNA secondary structure formation, GC content of the genome, role of G-quadruplex formation, and its relationship with radiosensitivity of the genome. MAJOR CONCLUSION In Deinococcus radiodurans, the bacterium that exhibits maximum radio resistance, multiple G-quadruplex forming motifs are reported. In human cells, G-quadruplex formation led to differential radiosensitivity. In this article, we have discussed, the role of secondary DNA structure formation like G-quadruplex in shielding the genome from radiation and its implications in understanding evolution of radio protective effect of an organism. We also discuss role of GC content and its correlation with radio resistance. GENERAL SIGNIFICANCE This review provides an insight into the role of G-quadruplexes in providing differential radiosensitivity at different site of the genome and in different organisms. It further discusses the possibility of higher GC content contributing towards reduced radiosensitivity in different organisms, evolution of radiosensitivity, and regulation of multiple cellular processes.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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Bartas M, Červeň J, Guziurová S, Slychko K, Pečinka P. Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins. Int J Mol Sci 2021; 22:ijms22020922. [PMID: 33477647 PMCID: PMC7831508 DOI: 10.3390/ijms22020922] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
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Gratal PB, Quero JG, Pérez-Redondo A, Gándara Z, Gude L. PhenQE8, a Novel Ligand of the Human Telomeric Quadruplex. Int J Mol Sci 2021; 22:E749. [PMID: 33451070 PMCID: PMC7828518 DOI: 10.3390/ijms22020749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 01/02/2023] Open
Abstract
A novel quadruplex ligand based on 1,10-phenanthroline and incorporating two guanyl hydrazone functionalities, PhenQE8, is reported herein. Synthetic access was gained in a two-step procedure with an overall yield of 61%. X-ray diffraction studies revealed that PhenQE8 can adopt an extended conformation that may be optimal to favor recognition of quadruplex DNA. DNA interactions with polymorphic G-quadruplex telomeric structures were studied by different techniques, such as Fluorescence resonance energy transfer (FRET) DNA melting assays, circular dichroism and equilibrium dialysis. Our results reveal that the novel ligand PhenQE8 can efficiently recognize the hybrid quadruplex structures of the human telomeric DNA, with high binding affinity and quadruplex/duplex selectivity. Moreover, the compound shows significant cytotoxic activity against a selected panel of cultured tumor cells (PC-3, HeLa and MCF-7), whereas its cytotoxicity is considerably lower in healthy human cells (HFF-1 and RPWE-1).
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Affiliation(s)
| | | | | | - Zoila Gándara
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
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Turcotte MA, Garant JM, Cossette-Roberge H, Perreault JP. Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson's disease. RNA Biol 2020; 18:1339-1353. [PMID: 33305682 PMCID: PMC8354592 DOI: 10.1080/15476286.2020.1847866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous system were initially identified and were found to be significantly enriched. Several G4 sequences found in the 5ʹ untranslated regions (5ʹUTR) of mRNAs associated with Parkinson’s disease were demonstrated to in fact fold in vitro by biochemical assays. Subcloning of the full-length 5ʹUTRs of these candidates upstream of a luciferase reporter system led to the demonstration that the G4s of both Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) significantly repressed the translation of both genes in SH-SY5Y cells. Subsequently, a strategy of using label-free RNA affinity purification assays with either of these two G4 sequences as bait isolated the Guanine Nucleotide-Binding Protein-Like 1 (GNL1). The latter was shown to have a higher affinity for the G4 sequences than for their mutated version. This study sheds light on new RNA G-quadruplexes located in genes dysregulated in Parkinson disease and a new G4-binding protein, GNL1.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Michel Garant
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Hélène Cossette-Roberge
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
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62
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Zhang JT, Wang LX, Yang FM, Yang L, Liu Y, Tang YL. Selective recognition of DNA parallel G-quadruplexes by 3,8a-disubstituted indolizinones. Bioorg Med Chem 2020; 29:115848. [PMID: 33189508 DOI: 10.1016/j.bmc.2020.115848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/25/2022]
Abstract
Owing to its potential biological relevance, DNA G-quadruplex has been considered as a prospective anti-cancer target. Some known G-quadruplex-interactive N-containing compounds with low cytotoxicity have become prospective anticancer drugs. Here we reported a new type of N-containing alkaloids 3,8a-disubstituted indolizinones, and investigated their substituent effects at 3- and 8a-positions in targeting to DNA c-myc G-quadruplex. And then we used 3-naphtyl-8a-(pyridin-2-yl) substrate I8 as an example, and investigated its ability in targeting to DNA parallel G-quadruplexes in vitro.
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Affiliation(s)
- Jing-Tao Zhang
- 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; Key Laboratory for Environmentally Friendly Chemistry and Application, Department of Chemistry, Xiangtan University, Hunan 411105, PR China
| | - Li-Xia Wang
- 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
| | - Feng-Min Yang
- 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
| | - Luo Yang
- Key Laboratory for Environmentally Friendly Chemistry and Application, Department of Chemistry, Xiangtan University, Hunan 411105, PR China
| | - Yan Liu
- 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
| | - Ya-Lin Tang
- 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; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
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63
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Gudanis D, Kaniowski D, Kulik K, Baranowski D, Gdaniec Z, Nawrot B. Formation of an RNA Quadruplex-Duplex Hybrid in Living Cells between mRNA of the Epidermal Growth Factor Receptor (EGFR) and a G-Rich Antisense Oligoribonucleotide. Cells 2020; 9:cells9112375. [PMID: 33138194 PMCID: PMC7692301 DOI: 10.3390/cells9112375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Antisense DNA oligonucleotides, short interfering RNAs (siRNAs), and CRISPR/Cas9 genetic tools are the most useful therapeutic nucleic acids regulating gene expression based on the antisense specificity towards messenger RNA. Here, we present an effective novel strategy for inhibiting translation based on the antisense-controlled formation of an RNA quadruplex-duplex hybrid (QDH) between a G-rich RNA antisense oligoribonucleotide (Q-ASO) and specific mRNA, comprising two distant G-tracts. We selected epidermal growth factor receptor (EGFR) as a well-established target protein in anticancer therapy. The chemically modified, bi-functional anti-EGFR Q-ASO and a 56-nt long EGFR mRNA fragment, in the presence of potassium ions, were shown to form in vitro very stable parallel G-quadruplex containing a 28-nt long external loop folding to two duplex-stem structure. Besides, the Q-ASOs effectively reduced EGFR mRNA levels compared to the non-modified RNA and DNA antisense oligonucleotides (rASO, dASO). In addition, the hybridization specificity of Q-ASO comprising a covalently attached fluorescent tag was confirmed in living cells by visualization of the G4 green fluorescent species in the presence of other antisense inhibitors under competitive conditions. The results presented here offer novel insights into the potential application of Q-ASOs for the detection and/or alteration of (patho)biological processes through RNA:RNA quadruplex-duplex formation in cellular systems.
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Affiliation(s)
- Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (D.B.); (Z.G.)
- Correspondence: ; Tel.: +48-61-852-85-03 (ext. 1286)
| | - Damian Kaniowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland; (D.K.); (K.K.); (B.N.)
| | - Katarzyna Kulik
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland; (D.K.); (K.K.); (B.N.)
| | - Daniel Baranowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (D.B.); (Z.G.)
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (D.B.); (Z.G.)
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland; (D.K.); (K.K.); (B.N.)
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64
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Cetin B, Wabl CA, Gumusay O. The DNA damaging revolution. Crit Rev Oncol Hematol 2020; 156:103117. [PMID: 33059228 DOI: 10.1016/j.critrevonc.2020.103117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/05/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme that plays a critical role in the repair of single-strand DNA damage via the base excision repair pathway. PARP inhibitors have substantial single-agent antitumor activity by inducing synthetic lethality. They have also emerged as promising anticancer targeted therapies, especially in tumors harboring deleterious germline or somatic breast cancer susceptibility gene (BRCA) mutations. PARP inhibition produces single-strand DNA breaks, which may be repaired by homologous recombination, a process partially dependent on BRCA1 and BRCA2. The PARP inhibitors olaparib, veliparib, talazoparib, niraparib, and rucaparib have predominantly been studied in patients with breast or ovarian cancers associated with deleterious germline mutations in BRCA1 and BRCA2. Ongoing clinical trials are evaluating the role of PARP inhibitors alone and in combination with other therapies, including selective inhibitors against key targets involved in the DNA damage response. In this review we summarize the use of PARP inhibitors in various tumor types, as well as possible approaches for overcoming resistance to PARP inhibitors.
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Affiliation(s)
- Bulent Cetin
- Department of Internal Medicine, Division of Medical Oncology, Suleyman Demirel University, Faculty of Medicine, Isparta, Turkey.
| | - Chiara A Wabl
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States
| | - Ozge Gumusay
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States
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65
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Umar MI, Kwok CK. Specific suppression of D-RNA G-quadruplex-protein interaction with an L-RNA aptamer. Nucleic Acids Res 2020; 48:10125-10141. [PMID: 32976590 PMCID: PMC7544233 DOI: 10.1093/nar/gkaa759] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4-protein interactions; however, until now there is no aptamer tool being developed to do so. Herein, we present a novel L-RNA aptamer that can generally bind to D-RNA G-quadruplex (rG4) structure, and interfere with rG4-protein interaction. Using hTERC rG4 as the target for in vitro selection, we report the shortest L-aptamer being developed so far, with only 25 nucleotides. Notably, this new aptamer, L-Apt.4-1c, adopts a stem-loop structure with the loop folding into an rG4 motif with two G-quartet, demonstrates preferential binding toward rG4s over non-G4s and DNA G-quadruplexes (dG4s), and suppresses hTERC rG4-nucleolin interactions. We also show that inhibition of rG4-protein interaction using L-RNA aptamer L-Apt.4-1c is comparable to or better than G4-specific ligands such as carboxypyridostatin and QUMA-1 respectively, highlighting that our approach and findings expand the current G4 toolbox, and open a new avenue for diverse applications.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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66
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Imperatore C, Varriale A, Rivieccio E, Pennacchio A, Staiano M, D’Auria S, Casertano M, Altucci C, Valadan M, Singh M, Menna M, Varra M. Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides. Int J Mol Sci 2020; 21:E7103. [PMID: 32993097 PMCID: PMC7582650 DOI: 10.3390/ijms21197103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
The synthesis of two 5'-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5'-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5'-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.
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Affiliation(s)
- Concetta Imperatore
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Antonio Varriale
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Elisa Rivieccio
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Angela Pennacchio
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Maria Staiano
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Sabato D’Auria
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Marcello Casertano
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Carlo Altucci
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Mohammadhassan Valadan
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Manjot Singh
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Marialuisa Menna
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Michela Varra
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
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67
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Brázda V, Luo Y, Bartas M, Kaura P, Porubiaková O, Šťastný J, Pečinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL. G-Quadruplexes in the Archaea Domain. Biomolecules 2020; 10:biom10091349. [PMID: 32967357 PMCID: PMC7565180 DOI: 10.3390/biom10091349] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/26/2022] Open
Abstract
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Yu Luo
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
| | - Otilia Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
- Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daniela Verga
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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68
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Ida J, Kuzuya A, Choong YS, Lim TS. An intermolecular-split G-quadruplex DNAzyme sensor for dengue virus detection. RSC Adv 2020; 10:33040-33051. [PMID: 35515051 PMCID: PMC9056686 DOI: 10.1039/d0ra05439a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/23/2020] [Indexed: 01/12/2023] Open
Abstract
Nucleic acids have special ability to organize themselves into various non-canonical structures, including a four-stranded DNA structure termed G-quadruplex (G4) that has been utilized for diagnostic and therapeutic applications. Herein, we report the ability of G4 to distinguish dengue virus (DENV) based on its serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) using a split G4-hemin DNAzyme configuration. In this system, two separate G-rich oligonucleotides are brought together upon target DNA strand hybridization to form a three-way junction architecture, allowing the formation of a G4 structure. The G4 formation in complexation with hemin can thus provide a signal readout by generating a DNAzyme that is able to catalyze H2O2-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS). This results in a change of color providing a sensing platform for the colorimetric detection of DENV. In our approach, betaine and dimethyl sulfoxide were utilized for better G4 generation by enhancing the target-probe hybridization. In addition to this serotype-specific assay, a multi-probe cocktail assay, which is an all-in-one assay was also examined for DENV detection. The system highlights the potential of split G-quadruplex configurations for the development of DNA-based detection and serotyping systems in the future.
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Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University 3-3-35 Yamate, Suita Osaka 564-8680 Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia 11800 Penang Malaysia
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69
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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: 12] [Impact Index Per Article: 3.0] [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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70
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He YD, Zheng KW, Wen CJ, Li XM, Gong JY, Hao YH, Zhao Y, Tan Z. Selective Targeting of Guanine-Vacancy-Bearing G-Quadruplexes by G-Quartet Complementation and Stabilization with a Guanine-Peptide Conjugate. J Am Chem Soc 2020; 142:11394-11403. [PMID: 32491844 DOI: 10.1021/jacs.0c00774] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stabilization of G-quadruplexes (G4s) formed in guanine-rich (G-rich) nucleic acids by small-molecule ligands has been extensively explored as a therapeutic approach for diseases such as cancer. Finding ligands with sufficient affinity and specificity toward G4s remains a challenge, and many ligands reported seemed to compromise between the two features. To cope with this challenge, we focused on targeting a particular type of G4s, i.e., the G-vacancy-bearing G-quadruplexes (GVBQs), by taking a structure complementation strategy to enhance both affinity and selectivity. In this approach, a G-quadruplex-binding peptide RHAU23 is guided toward a GVBQ by a guanine moiety covalently linked to the peptide. The filling-in of the vacancy in a GVBQ by the guanine ensures an exclusive recognition of GVBQ. Moreover, the synergy between the RHAU23 and the guanine dramatically improves both the affinity toward and stabilization of the GVBQ. Targeting a GVBQ in DNA by this bifunctional peptide strongly suppresses in vitro replication. This study demonstrates a novel and promising alternative targeting strategy to a distinctive panel of G4s that are as abundant as the canonical ones in the human genome.
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Affiliation(s)
- Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Ke-Wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Cui-Jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Xin-Min Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jia-Yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Yu-Hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | | | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China.,Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P. R. China
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71
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G-quadruplex, Friend or Foe: The Role of the G-quartet in Anticancer Strategies. Trends Mol Med 2020; 26:848-861. [PMID: 32467069 DOI: 10.1016/j.molmed.2020.05.002] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The clinical applicability of G-quadruplexes (G4s) as anticancer drugs is currently being evaluated. Several G4 ligands and aptamers are undergoing clinical trials following the notable examples of quarfloxin and AS1411, respectively. In this review, we summarize the latest achievements and breakthroughs in the use of G4 nucleic acids as both therapeutic tools ('friends', as healing anticancer drugs) and targets ('foes', within the harmful cancer cell), particularly using aptamers and quadruplex-targeted ligands, respectively. We explore the recent research on synthetic G4 ligands toward the discovery of anticancer therapeutics and their mechanism of action. Additionally, we highlight recent advances in chemical and structural biology that enable the design of specific G4 aptamers to be used as novel anticancer agents.
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Wen CJ, Gong JY, Zheng KW, He YD, Zhang JY, Hao YH, Tan Z. Targeting nucleic acids with a G-triplex-to-G-quadruplex transformation and stabilization using a peptide-PNA G-tract conjugate. Chem Commun (Camb) 2020; 56:6567-6570. [PMID: 32396929 DOI: 10.1039/d0cc02102d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A dual-functional peptide-PNA (peptide nucleic acid) conjugate consisting of a PNA G3-tract and an RHAU23 peptide is devised to target nucleic acids bearing three tandem guanine tracts (G-tracts). The PNA G3-tract joins the three G-tracts to form a stable bimolecular G-quadruplex (G4) and the resulting G4 is then bound by the RHAU23 moiety to form an extra stable G4-peptide complex. Owing to this synergistic dual structural enforcement, the conjugate accomplished extremely high selectivity and nM to sub-nM affinities towards its targets that are up to 1000 times greater than the small molecule G4 ligands. As a result, the conjugate impacts the tracking activity of motor proteins on DNA with superior selectivity and potency that are rarely seen in other G4-targeting approaches.
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Affiliation(s)
- Cui-Jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
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73
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Xi M, Li Y, Zhou J. Exploration of the formation and structure characteristics of a miR-92a promoter G-quadruplex by ESI-MS and CD. Talanta 2020; 211:120708. [PMID: 32070614 DOI: 10.1016/j.talanta.2019.120708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/24/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022]
Abstract
Combining electrospray ionization mass spectrometry (ESI-MS) with circular dichroism (CD) spectroscopy, a G-rich sequence from miR-92a promoter region was discovered to form a parallel G-quadruplex structures in KCl or NH4OAc solution. In case of high concentration of NH4OAc, the ESI mass spectra showed peaks of a dimeric G-quadruplex structure with 4 ammonium ions. Meanwhile, palmatine, a natural alkaloid, was screened by ESI-MS to bind with the miR-92a G-quadruplex affinitively. The variable temperature experiment of CD also proved that high concentration of NH4OAc or palmatine could promote the stability of the dimeric G-quadruplex structure. To get the specific characteristics of the miR-92a G-quadruplex structure, systematic mutations of guanine were tested. Based on the number of NH4+ or ligands, the important guanines involved in the G-quadruplex could be determined. Considering the importance of involved guanines and the number of G-quartets, we speculated an interlocked dimeric parallel G-quadruplex as a possible conformation of the miR-92a promoter G-quadruplex. All results obtained from ESI-MS and CD illustrate structure characteristics of the miR-92a G-quadruplex, which is a promising method for preliminary structural analysis of G-quadruplexes. Besides, this study also provides a strategy for regulating the functions of microRNA by exploring and targeting higher-order structures of miRNAs.
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Affiliation(s)
- Min Xi
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China; Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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74
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Di Fonzo S, Amato J, D'Aria F, Caterino M, D'Amico F, Gessini A, Brady JW, Cesàro A, Pagano B, Giancola C. Ligand binding to G-quadruplex DNA: new insights from ultraviolet resonance Raman spectroscopy. Phys Chem Chem Phys 2020; 22:8128-8140. [PMID: 32246758 DOI: 10.1039/d0cp01022g] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-Quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of several biological processes of many organisms. The rational design of G4-targeting molecules developed as potential anticancer and antiviral therapeutics is a complex problem intrinsically due to the structural polymorphism of these peculiar DNA structures. The aim of the present work is to show how Ultraviolet Resonance Raman (UVRR) spectroscopy can complement other techniques in providing valuable information about ligand/G4 interactions in solution. Here, the binding of BRACO-19 and Pyridostatin - two of the most potent ligands - to selected biologically relevant G4s was investigated by polarized UVRR scattering at 266 nm. The results give new insights into the binding mode of these ligands to G4s having different sequences and topologies by performing an accurate analysis of peaks assigned to specific groups and their changes upon binding. Indeed, the UVRR data not only show that BRACO-19 and Pyridostatin interact with different G4 sites, but also shed light on the ligand and G4 chemical groups really involved in the interaction. In addition, UVRR results complemented by circular dichroism data clearly indicate that the binding mode of a ligand can also depend on the conformation(s) of the target G4. Overall, these findings demonstrate the utility of using UVRR spectroscopy in the investigation of G4s and G4-ligand interactions in solution.
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Affiliation(s)
- Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Marco Caterino
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Francesco D'Amico
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York, NY 14853, USA
| | - Attilio Cesàro
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy. and Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, I-34127, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
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75
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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76
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Tyagi S, Saxena S, Kundu N, Sharma T, Chakraborty A, Kaur S, Miyoshi D, Shankaraswamy J. Selective recognition of human telomeric G-quadruplex with designed peptide via hydrogen bonding followed by base stacking interactions. RSC Adv 2019; 9:40255-40262. [PMID: 35542665 PMCID: PMC9076235 DOI: 10.1039/c9ra08761c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 01/10/2023] Open
Abstract
We described a novel synthetic peptide in which a glutamine residue binds through hydrogen bonding to a guanine-base and a trytophan residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over its complementary c-rich strand and a double-stranded DNA and its complementary C-rich strand. This peptide offers great potential for cancer treatment by inhibiting the telomere extension by telomerase. A new synthetic peptide is presented. A Glu residue binds through H-bonding to a guanine-base and a Trp residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over a complementary c-rich strand and double-stranded DNA.![]()
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Affiliation(s)
- Shikhar Tyagi
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201303 India +91-120-4735600
| | - Sarika Saxena
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201303 India +91-120-4735600
| | - Nikita Kundu
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201303 India +91-120-4735600
| | - Taniya Sharma
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201303 India +91-120-4735600
| | - Amlan Chakraborty
- Department of Chemical Engineering, Monash University Clayton VIC 3800 Australia
| | - Sarvpreet Kaur
- Structural Biology Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh Sector-125, Expressway Highway Noida 201303 India +91-120-4735600
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University 7-1-20 Minatojima-minamimachi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Mojerla, Sri Konda Laxman Telangana State Horticultural University 509382 Telangana India
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77
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Bartas M, Čutová M, Brázda V, Kaura P, Šťastný J, Kolomazník J, Coufal J, Goswami P, Červeň J, Pečinka P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. Molecules 2019; 24:molecules24091711. [PMID: 31052562 PMCID: PMC6539912 DOI: 10.3390/molecules24091711] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/09/2023] Open
Abstract
The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Michaela Čutová
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
| | - Václav Brázda
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Kolomazník
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Pratik Goswami
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jiří Červeň
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
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