51
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Zhang L, Liu X, Lu S, Liu J, Zhong S, Wei Y, Bing T, Zhang N, Shangguan D. Thiazole Orange Styryl Derivatives as Fluorescent Probes for G-Quadruplex DNA. ACS APPLIED BIO MATERIALS 2020; 3:2643-2650. [DOI: 10.1021/acsabm.9b01243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Lingling Zhang
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Guangxi Medical University, No. 22, Shuangyong Road, Nanning 530021, Guangxi, PR China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Lu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilong Zhong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yongbiao Wei
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Guangxi Medical University, No. 22, Shuangyong Road, Nanning 530021, Guangxi, PR China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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52
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Ly L, Chan D, Landry M, Angle C, Martel J, Trasler J. Impact of mothers' early life exposure to low or high folate on progeny outcome and DNA methylation patterns. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa018. [PMID: 33240529 PMCID: PMC7673481 DOI: 10.1093/eep/dvaa018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/03/2020] [Accepted: 09/19/2020] [Indexed: 05/14/2023]
Abstract
The dynamic patterning of DNA and histone methylation during oocyte development presents a potentially susceptible time for epigenetic disruption due to early life environmental exposure of future mothers. We investigated whether maternal exposure to folic acid deficient and supplemented diets starting in utero could affect oocytes and cause adverse developmental and epigenetic effects in next generation progeny. Female BALB/c mice (F0) were placed on one of four amino acid defined diets for 4 weeks before pregnancy and throughout gestation and lactation: folic acid control (rodent recommended daily intake; Ctrl), 7-fold folic acid deficient, 10-fold folic acid supplemented or 20-fold folic acid supplemented diets. F1 female pups were weaned onto Ctrl diets, mated to produce the F2 generation and the F2 offspring were examined at E18.5 for developmental and epigenetic abnormalities. Resorption rates were increased and litter sizes decreased amongst F2 E18.5-day litters in the 20-fold folic acid supplemented group. Increases in abnormal embryo outcomes were observed in all three folic acid deficient and supplemented groups. Subtle genome-wide DNA methylation alterations were found in the placentas and brains of F2 offspring in the 7-fold folic acid deficient , 10-fold folic acid supplemented and 20-fold folic acid supplemented groups; in contrast, global and imprinted gene methylation were not affected. The findings show that early life female environmental exposures to both low and high folate prior to oocyte maturation can compromise oocyte quality, adversely affecting offspring of the next generation, in part by altering DNA methylation patterns.
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Affiliation(s)
- Lundi Ly
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mylène Landry
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Camille Angle
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Correspondence address. Research Institute of the McGill University Health Centre, 1001 Boulevard Décarie, Block E.M.0.3211, Montreal, QC, Canada H4A 3J1. Tel: +1-514-934-1934 (ext. 25235); Fax: +1-514-933-9673; E-mail:
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53
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Saad M, Guédin A, Amor S, Bedrat A, Tourasse NJ, Fayyad-Kazan H, Pratviel G, Lacroix L, Mergny JL. Mapping and characterization of G-quadruplexes in the genome of the social amoeba Dictyostelium discoideum. Nucleic Acids Res 2019; 47:4363-4374. [PMID: 30923812 PMCID: PMC6511855 DOI: 10.1093/nar/gkz196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 01/25/2023] Open
Abstract
G-quadruplexes (G4) are non-canonical DNA and/or RNA secondary structures formed in guanine-rich regions. Given their over-representation in specific regions in the genome such as promoters and telomeres, they are likely to play important roles in key processes such as transcription, replication or RNA maturation. Putative G4-forming sequences (G4FS) have been reported in humans, yeast, bacteria, viruses and many organisms. Here we present the first mapping of G-quadruplex sequences in Dictyostelium discoideum, the social amoeba. ‘Dicty’ is an ameboid protozoan with a small (34 Mb) and extremely AT rich genome (78%). As a consequence, very few G4-prone motifs are expected. An in silico analysis of the Dictyostelium genome with the G4Hunter software detected 249–1055 G4-prone motifs, depending on G4Hunter chosen threshold. Interestingly, despite an even lower GC content (as compared to the whole Dicty genome), the density of G4 motifs in Dictyostelium promoters and introns is significantly higher than in the rest of the genome. Fourteen selected sequences located in important genes were characterized by a combination of biophysical and biochemical techniques. Our data show that these sequences form highly stable G4 structures under physiological conditions. Five Dictyostelium genes containing G4-prone motifs in their promoters were studied for the effect of a new G4-binding porphyrin derivative on their expression. Our results demonstrated that the new ligand significantly decreased their expression. Overall, our results constitute the first step to adopt Dictyostelium discoideum as a ‘G4-poor’ model for studies on G-quadruplexes.
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Affiliation(s)
- Mona Saad
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.,Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Beirut, Al-Hadath, Lebanon, Lebanon
| | - Aurore Guédin
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Souheila Amor
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Amina Bedrat
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Nicolas J Tourasse
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Hussein Fayyad-Kazan
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Beirut, Al-Hadath, Lebanon, Lebanon
| | | | | | - Jean-Louis Mergny
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.,Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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54
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Gray LT, Puig Lombardi E, Verga D, Nicolas A, Teulade-Fichou MP, Londoño-Vallejo A, Maizels N. G-quadruplexes Sequester Free Heme in Living Cells. Cell Chem Biol 2019; 26:1681-1691.e5. [PMID: 31668518 DOI: 10.1016/j.chembiol.2019.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/13/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
Heme is an essential cofactor for many enzymes, but free heme is toxic and its levels are tightly regulated. G-quadruplexes bind heme avidly in vitro, raising the possibility that they may sequester heme in vivo. If so, then treatment that displaces heme from quadruplexes is predicted to induce expression of genes involved in iron and heme homeostasis. Here we show that PhenDC3, a G-quadruplex ligand structurally unrelated to heme, displaces quadruplex-bound heme in vitro and alters transcription in cultured human cells, upregulating genes that support heme degradation and iron homeostasis, and most strikingly causing a 30-fold induction of heme oxidase 1, the key enzyme in heme degradation. We propose that G-quadruplexes sequester heme to protect cells from the pathophysiological consequences of free heme.
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Affiliation(s)
- Lucas T Gray
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Emilia Puig Lombardi
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris 75005, France
| | - Daniela Verga
- Institut Curie, Centre de Recherche, CNRS-UMR9187, INSERM-U1196, PSL Research University, Sorbonne Universités, Orsay 91405, France; CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay 91405, France
| | - Alain Nicolas
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris 75005, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, Centre de Recherche, CNRS-UMR9187, INSERM-U1196, PSL Research University, Sorbonne Universités, Orsay 91405, France; CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay 91405, France
| | - Arturo Londoño-Vallejo
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris 75005, France
| | - Nancy Maizels
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.
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55
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Jara-Espejo M, Line SR. DNA G-quadruplex stability, position and chromatin accessibility are associated with CpG island methylation. FEBS J 2019; 287:483-495. [PMID: 31532882 DOI: 10.1111/febs.15065] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/22/2019] [Accepted: 09/16/2019] [Indexed: 01/06/2023]
Abstract
CpG islands (CGI) are genomic regions associated with gene promoters and involved in gene expression regulation. Despite their high CpG content and unlike bulk genomic DNA methylation pattern, these regions are usually hypomethylated. So far, the mechanisms controlling the CGI methylation patterning remain unclear. G-quadruplex (G4) structures can inhibit DNA methyltransferases 1 enzymatic activity, leading to CGI hypomethylation. Our aim was to analyse the association of G4 forming sequences (G4FS) and CGI methylation as well as to determine the intrinsic and extrinsic characteristics of G4FS that may modulate this phenomenon. Using methylation data from human embryonic stem cells (hESCs) and three hESC-derived populations, we showed that hypomethylated CpGs located inside CGI (CGI/CpG) tend to be associated with highly stable G4FS (Minimum free energy ≤ -30 kcal·mol-1 ). The association of highly stable G4FS and hypomethylation tend to be stronger when these structures are located at shorter distances (~ < 150 bp) from GCI/CpGs, when G4FS and CpGs are located within open chromatin and G4FS are inside CGI. Moreover, this association is not strongly influenced by the CpG content of CGI. Conversely, highly methylated CGI/CpG tend to be associated with low stability G4FS. Although CpGs inside CGIs without a G4FS tend to be more methylated, high stability G4FS within CGI neighbourhood were associated with decreased methylation. In summary, our data indicate that G4FS may act as protective cis elements against CGI methylation, and this effect seems to be influenced by the G4FS folding potential, its presence within CGI, CpG distance from G4FS and chromatin accessibility.
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Affiliation(s)
- Manuel Jara-Espejo
- Department of Morphology, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, Brazil
| | - Sérgio Roberto Line
- Department of Morphology, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, Brazil
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56
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Beltran M, Tavares M, Justin N, Khandelwal G, Ambrose J, Foster BM, Worlock KB, Tvardovskiy A, Kunzelmann S, Herrero J, Bartke T, Gamblin SJ, Wilson JR, Jenner RG. G-tract RNA removes Polycomb repressive complex 2 from genes. Nat Struct Mol Biol 2019; 26:899-909. [PMID: 31548724 PMCID: PMC6778522 DOI: 10.1038/s41594-019-0293-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/05/2019] [Indexed: 12/15/2022]
Abstract
Polycomb Repressive Complex 2 (PRC2) maintains repression of cell type-specific genes but also associates with genes ectopically in cancer. While it is currently unknown how PRC2 is removed from genes, such knowledge would be useful for the targeted reversal of deleterious PRC2 recruitment events. Here, we show that G-tract RNA specifically removes PRC2 from genes in human and mouse cells. PRC2 preferentially binds G-tracts within nascent pre-mRNAs, especially within predicted G-quadruplex structures. G-quadruplex RNA evicts the PRC2 catalytic core from the substrate nucleosome. PRC2 transfers from chromatin to RNA upon gene activation and chromatin-associated G-tract RNA removes PRC2, leading to H3K27me3 depletion from genes. Targeting G-tract RNA to the tumor suppressor gene CDKN2A in malignant rhabdoid tumor cells reactivates the gene and induces senescence. These data support a model in which pre-mRNA evicts PRC2 during gene activation and provides the means to selectively remove PRC2 from specific genes.
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Affiliation(s)
- Manuel Beltran
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | - Manuel Tavares
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | | | - Garima Khandelwal
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | - John Ambrose
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK.,Genomics England, London, UK
| | - Benjamin M Foster
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kaylee B Worlock
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Javier Herrero
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Richard G Jenner
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK.
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57
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Bryan TM. Mechanisms of DNA Replication and Repair: Insights from the Study of G-Quadruplexes. Molecules 2019; 24:E3439. [PMID: 31546714 PMCID: PMC6804030 DOI: 10.3390/molecules24193439] [Citation(s) in RCA: 55] [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: 08/13/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes are four-stranded guanine-rich structures that have been demonstrated to occur across the genome in humans and other organisms. They provide regulatory functions during transcription, translation and immunoglobulin gene rearrangement, but there is also a large amount of evidence that they can present a potent barrier to the DNA replication machinery. This mini-review will summarize recent advances in understanding the many strategies nature has evolved to overcome G-quadruplex-mediated replication blockage, including removal of the structure by helicases or nucleases, or circumventing the deleterious effects on the genome through homologous recombination, alternative end-joining or synthesis re-priming. Paradoxically, G-quadruplexes have also recently been demonstrated to provide a positive role in stimulating the initiation of DNA replication. These recent studies have not only illuminated the many roles and consequences of G-quadruplexes, but have also provided fundamental insights into the general mechanisms of DNA replication and its links with genetic and epigenetic stability.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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58
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Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail. PLoS Comput Biol 2019; 15:e1007383. [PMID: 31539370 PMCID: PMC6774569 DOI: 10.1371/journal.pcbi.1007383] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/02/2019] [Accepted: 09/09/2019] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order G4 DNA structures. To understand the molecular driving forces for G4 association, here, we study the binding interaction between two parallel-stranded G-quadruplexes using all-atom molecular dynamics simulations. The predicted dimerization free energies show that direct binding through the 5’-G-tetrads is the most preferred of all possible end-to-end stacking orientations, consistently with all available experimental data. Decomposition of dimerization enthalpies in combination with simulations at varying ionic strength further indicate that the observed orientational preferences arise from a fine balance between the electrostatic repulsion of the sugar-phosphate backbones and favorable counterion binding at the dimeric interface. We also demonstrate how these molecular-scale findings can be used to devise means of controlling G4 dimerization equilibrium, e.g., by altering salt concentration and using G4-targeted ligands. Native DNA usually folds to form the canonical double helix, however, under certain conditions, it can also fold into other secondary structures. Some of the most interesting ones are G-quadruplexes (G4)—compact DNA structures in which guanines assemble into multilayered tetrads, and whose formation has been reported at the ends of linear chromosomes (telomeres) and at different regulatory regions of the genome. Although structural and basic energetic properties, as well as some biological functions of G-quadruplexes are quite well understood, not much is known about their propensity to form agregated structures. A very high density of G-quadruplexes at telomeres along with their large exposed planar surfaces indeed favor G4 aggregation through end-to-end stacking, which might be important for the protection of telomeres and DNA packaging. In this research, using computer simulations, we provide insight into molecular origins of stability of the higher-order G-quadruplexes and explain in structural and energetic terms a strong preference for one particular end-to-end stacking orientation. Based on the recognized aggregation driving forces, we also suggest methods for controling the aggregation preferences openining up new opportunities for designing oligomeric G-quadruplexes.
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59
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Wan C, Fu W, Jing H, Zhang N. NMR solution structure of an asymmetric intermolecular leaped V-shape G-quadruplex: selective recognition of the d(G2NG3NG4) sequence motif by a short linear G-rich DNA probe. Nucleic Acids Res 2019; 47:1544-1556. [PMID: 30445650 PMCID: PMC6379650 DOI: 10.1093/nar/gky1167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023] Open
Abstract
Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itself distinctive and thus an essentially more accessible target. As an alternative to the conventional antisense method using a complementary chain, forming an intermolecular G-quadruplex from two different oligomers, in which the longer one as the target is captured by a short G-rich fragment, could be helpful for recognizing G-rich sequences and structural motifs. However, such an intermolecular leaped V-shape G-quadruplex consisting of DNA oligomers of quite different lengths has not been evaluated. Here, we present the first nuclear magnetic resonance (NMR) study of an asymmetric intermolecular leaped V-shape G-quadruplex assembled between an Oxytricha nova telomeric sequence d(G2T4G4T4G4) and a single G-tract fragment d(TG4A). Furthermore, we explored the selectivity of this short fragment as a potential probe, examined the kinetic discrimination for probing a specific mutant, and proposed the key sequence motif d(G2NG3NG4) essential for building the leaped V-shape G-quadruplexes.
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Affiliation(s)
- Chanjuan Wan
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China
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60
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Puig Lombardi E, Holmes A, Verga D, Teulade-Fichou MP, Nicolas A, Londoño-Vallejo A. Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species. Nucleic Acids Res 2019; 47:6098-6113. [PMID: 31114920 PMCID: PMC6614823 DOI: 10.1093/nar/gkz463] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/29/2022] Open
Abstract
G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.
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Affiliation(s)
| | - Allyson Holmes
- Institut Curie, PSL Research University, UMR3244 CNRS, 75005 Paris, France
| | - Daniela Verga
- Institut Curie, PSL Research University, Sorbonne Universités, UPMC, CNRS, Inserm, UMR9187/U1196, 91495 Orsay, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, Sorbonne Universités, UPMC, CNRS, Inserm, UMR9187/U1196, 91495 Orsay, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, UMR3244 CNRS, 75005 Paris, France
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61
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Herdy B, Mayer C, Varshney D, Marsico G, Murat P, Taylor C, D'Santos C, Tannahill D, Balasubramanian S. Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts. Nucleic Acids Res 2019; 46:11592-11604. [PMID: 30256975 PMCID: PMC6265444 DOI: 10.1093/nar/gky861] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/12/2018] [Indexed: 12/23/2022] Open
Abstract
RNA G-quadruplexes (rG4s) are secondary structures in mRNAs known to influence RNA post-transcriptional mechanisms thereby impacting neurodegenerative disease and cancer. A detailed knowledge of rG4–protein interactions is vital to understand rG4 function. Herein, we describe a systematic affinity proteomics approach that identified 80 high-confidence interactors that assemble on the rG4 located in the 5′-untranslated region (UTR) of the NRAS oncogene. Novel rG4 interactors included DDX3X, DDX5, DDX17, GRSF1 and NSUN5. The majority of identified proteins contained a glycine-arginine (GAR) domain and notably GAR-domain mutation in DDX3X and DDX17 abrogated rG4 binding. Identification of DDX3X targets by transcriptome-wide individual-nucleotide resolution UV-crosslinking and affinity enrichment (iCLAE) revealed a striking association with 5′-UTR rG4-containing transcripts which was reduced upon GAR-domain mutation. Our work highlights hitherto unrecognized features of rG4 structure–protein interactions that highlight new roles of rG4 structures in mRNA post-transcriptional control.
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Affiliation(s)
- Barbara Herdy
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands.,Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK
| | - Dhaval Varshney
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Giovanni Marsico
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Pierre Murat
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.,Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK
| | - Chris Taylor
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.,Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.,Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK
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62
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Uda RM, Nishimoto N, Matsui T, Takagi S. Photoinduced binding of malachite green copolymer to parallel G-quadruplex DNA. SOFT MATTER 2019; 15:4454-4459. [PMID: 31073583 DOI: 10.1039/c9sm00411d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Designing ligands that selectively target G-quadruplex DNAs has gained attention due to their possible roles in regulation of gene expression and as anti-cancer agents. In this article, we report irradiation-induced ligand binding to G-quadruplex DNAs which offers a novel approach to targeting specific G-quadruplexes. Photoinduced binding to G-quadruplex DNAs was observed for copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG). This molecule has an aromatic ring with cationic charge, which after irradiation becomes a binding site for G-quadruplex DNA. PVAMGs acted as neutral polymers with no binding affinity under dark conditions. The photoinduced binding was revealed by fluorescence spectroscopy, NMR spectroscopy, UV melting curve, and DNA polymerase stop assay. PVAMGs showed preference to parallel G-quadruplex structures over mixed parallel/antiparallel structures. PVAMGs were found to be noncytotoxic under both dark and irradiated conditions up to a concentration of 20 μM.
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Affiliation(s)
- Ryoko M Uda
- Department of Chemical Engineering, National Institute of Technology, Nara college, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
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63
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Tippana R, Chen MC, Demeshkina NA, Ferré-D'Amaré AR, Myong S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat Commun 2019; 10:1855. [PMID: 31015431 PMCID: PMC6478676 DOI: 10.1038/s41467-019-09802-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
DHX36 is a DEAH-box helicase that resolves parallel G-quadruplex structures formed in DNA and RNA. The recent co-crystal structure of DHX36 bound G4-DNA revealed an intimate contact, but did not address the role of ATP hydrolysis in G4 resolving activity. Here, we demonstrate that unlike on G4-DNA, DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, generating a highly asymmetric pattern of activity. Interestingly, DHX36 refolds G4-RNA in several steps, reflecting the discrete steps in forming the G4 structure. We show that the ATP-dependent activity of DHX36 arises from the RNA tail rather than the G4. Mutations that perturb G4 contact result in quick dissociation of the protein from RNA upon ATP hydrolysis, while mutations that interfere with binding the RNA tail induce dysregulated activity. We propose that the ATP-dependent activity of DHX36 may be useful for dynamically resolving various G4-RNA structures in cells.
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Affiliation(s)
- Ramreddy Tippana
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael C Chen
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1TN, UK.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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64
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G-Quadruplexes in Human Ribosomal RNA. J Mol Biol 2019; 431:1940-1955. [PMID: 30885721 DOI: 10.1016/j.jmb.2019.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022]
Abstract
rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.
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65
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Obstetric complication-associated ANXA5 promoter polymorphisms may affect gene expression via DNA secondary structures. J Hum Genet 2019; 64:459-466. [PMID: 30796324 DOI: 10.1038/s10038-019-0578-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 01/25/2023]
Abstract
Recent findings have highlighted the possibility that polymorphisms within the annexin A5 gene (ANXA5) promoter contribute to the etiology of various obstetric complications. However, the underlying mechanisms are unknown. The M2 haplotype of the ANXA5 shows lower activity and less expression of ANXA5 mRNA. This gene promoter region has a motif that potentially forms a G-quadruplex structure. In vitro G-quadruplex propensity estimated by circular dichroism indicated that the M2 haplotype oligonucleotide manifested a decreased potential for G-quadruplex formation. In addition, in vivo G-quadruplex formation of the promoter region was evidenced by the presence of single-stranded DNA shown by sodium bisulfite treatment of placental genomic DNA. Comparative analysis indicated less potential in the M2 allele than the major allele. Promoter activity of the two haplotypes determined by luciferase reporter analysis correlated with the estimated G-quadruplex propensity. Our data lend support to the developing paradigm that genomic variation affects gene expression levels via DNA secondary structures leading to the disease susceptibility.
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66
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Mirihana Arachchilage G, Hetti Arachchilage M, Venkataraman A, Piontkivska H, Basu S. Stable G-quadruplex enabling sequences are selected against by the context-dependent codon bias. Gene 2019; 696:149-161. [PMID: 30753890 DOI: 10.1016/j.gene.2019.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The distributions of secondary structural elements appear to differ between coding regions (CDS) of mRNAs compared to the untranslated regions (UTRs), presumably as a mechanism to fine-tune gene expression, including efficiency of translation. However, a systematic and comprehensive analysis of secondary structure avoidance because of potential bias in codon usage is difficult as some of the common secondary structures, such as, hairpins can be formed by numerous sequence combinations. Using G-quadruplex (GQ) as the model secondary structure we studied the impact of codon bias on GQs within the CDS. Because GQs can be predicted using specific consensus sequence motifs, they provide an excellent platform for investigation of the selectivity of such putative structures at the codon level. Using a bioinformatics approach, we calculated the frequencies of putative GQs within the CDS of a variety of species. Our results suggest that the most stable GQs appear to be significantly underrepresented within the CDS, through the use of specific synonymous codon combinations. Furthermore, we identified many peptide sequence motifs in which silent mutations can potentially alter translation via stable GQ formation. This work not only provides a comprehensive analysis on how stable secondary structures appear to be avoided within the CDS of mRNA, but also broadens the current understanding of synonymous codon usage as they relate to the structure-function relationship of RNA.
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Affiliation(s)
| | | | - Aparna Venkataraman
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States of America
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America.
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67
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Bian WX, Xie Y, Wang XN, Xu GH, Fu BS, Li S, Long G, Zhou X, Zhang XL. Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication. Nucleic Acids Res 2019; 47:56-68. [PMID: 30462330 PMCID: PMC6326805 DOI: 10.1093/nar/gky1177] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/22/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV core RNA G4 and host cellular proteins, and the roles of the HCV core RNA G4 in HCV infection and pathogenesis remain elusive. Here, we identified a cellular protein, nucleolin (NCL), which bound and stabilized the HCV core RNA G4 structure. We demonstrated the direct interaction and colocalization between NCL and wild-type core RNA G4 at both in vitro and in cell physiological conditions of the alive virus; however no significant interaction was found between NCL and G4-modified core RNA. NCL is also associated with HCV particles. HCV infection induced NCL mRNA and protein expression, while NCL suppressed wild-type viral replication and expression, but not G4-modified virus. Silencing of NCL greatly enhanced viral RNA replication. Our findings provide new insights that NCL may act as a host factor for anti-viral innate immunity, and binding of cellular NCL with the viral core RNA G4 structure is involved in suppressing HCV replication.
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Affiliation(s)
- Wen-Xiu Bian
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Yan Xie
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Xiao-Ning Wang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Hua Xu
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Bo-Shi Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Shu Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
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68
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Ko E, Kim JS, Ju S, Seo HW, Chang Y, Kang JA, Park SG, Jung G. Oxidatively Modified Protein-Disulfide Isomerase-Associated 3 Promotes Dyskerin Pseudouridine Synthase 1-Mediated Malignancy and Survival of Hepatocellular Carcinoma Cells. Hepatology 2018; 68:1851-1864. [PMID: 29672884 DOI: 10.1002/hep.30039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/26/2018] [Accepted: 04/16/2018] [Indexed: 12/14/2022]
Abstract
Dyskerin pseudouridine synthase 1 (DKC1) is a conserved gene encoding the RNA-binding protein dyskerin, which is an essential component of the telomerase holoenzyme. DKC1 up-regulation is frequently observed in many different human cancers including hepatocellular carcinoma (HCC); however, its regulatory mechanisms remain unclear. Thus, we investigated the regulatory mechanism of DKC1 in HCC progression. We found that protein-disulfide isomerase-associated 3 (PDIA3) interacted with the DKC1 regulatory DNA in HCC cells but not in HCC cells with elevated reactive oxygen species (ROS) levels, using liquid chromatographic-tandem mass spectrometric analysis after isolating the DKC1 regulatory region binding proteins. PDIA3 repressed DKC1 expression in HCC cells by recognizing the G-quadruplex DNA at the DKC1 location. However, oxidative modification of PDIA3 induced by ROS redistributed this protein into the cytosolic regions, which stimulated DKC1 expression. We also identified Met338 in PDIA3 as the oxidatively modified residue and validated the effect of oxidative modification using an ectopic expression system, a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 knock-in system, and a xenograft mouse model. We observed that oxidatively modified PDIA3 promoted DKC1-mediated malignancy and survival of HCC cells in vitro and in vivo. HCC tissues showed a positive association with ROS, cytoplasmic PDIA3, and nuclear DKC1 levels. HCC patients with high PDIA3 protein and DKC1 mRNA levels also displayed reduced recurrence-free survival rates. Cumulatively, the results showed that cytoplasmic PDIA3 activity could be essential in raising DKC1 expression in HCC progression and predicting poor prognoses in HCC patients. Conclusion: Our study indicates that the elevated ROS levels in HCC modulate cytoplasmic PDIA3 levels, resulting in HCC cell survival through DKC1 up-regulation.
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Affiliation(s)
- Eunkyong Ko
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Republic of Korea
| | - Jong-Seo Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Republic of Korea.,Center for RNA Research, Institute of Basic Science, Seoul, Republic of Korea
| | - Soomi Ju
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Republic of Korea.,Center for RNA Research, Institute of Basic Science, Seoul, Republic of Korea
| | - Hyun-Wook Seo
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Republic of Korea
| | - Yeonji Chang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Republic of Korea
| | - Jung-Ah Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Sung-Gyoo Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Guhung Jung
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Republic of Korea
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69
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A Fragment-Based Approach for the Development of G-Quadruplex Ligands: Role of the Amidoxime Moiety. Molecules 2018; 23:molecules23081874. [PMID: 30060461 PMCID: PMC6222391 DOI: 10.3390/molecules23081874] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022] Open
Abstract
G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed against the major G4 present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), the stabilization of which has been shown to suppress viral gene expression and replication. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We screened 150 small molecules, composed by structurally and chemically different fragments, selected from commercially available and in-house compounds; synthetic elaboration yielded several G4 ligands and two final G4 binders, both embedding an amidoxime moiety; one of these two compounds showed preferential binding for the HIV-1 LTR G4. This work presents the discovery of a novel potential pharmacophore and highlights the possibility to apply a fragment-based approach to develop G4 ligands with unexpected chemical features.
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70
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Pont I, González-García J, Inclán M, Reynolds M, Delgado-Pinar E, Albelda MT, Vilar R, García-España E. Aza-Macrocyclic Triphenylamine Ligands for G-Quadruplex Recognition. Chemistry 2018; 24:10850-10858. [DOI: 10.1002/chem.201802077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/14/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Isabel Pont
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Jorge González-García
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Mario Inclán
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
| | - Matthew Reynolds
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Estefanía Delgado-Pinar
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
| | - M. Teresa Albelda
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
- GIBI2030, Grupo de Investigación Biomédica en Imagen, IIS La Fe; Valencia Spain
| | - Ramon Vilar
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
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71
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Harikrishna S, Kotaru S, Pradeepkumar PI. Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design. MOLECULAR BIOSYSTEMS 2018. [PMID: 28650023 DOI: 10.1039/c7mb00175d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Stabilization of a G-quadruplex (G4) DNA structure in the proto-oncogene c-MYC using small molecule ligands has emerged as an attractive strategy for the development of anticancer therapeutics. To understand the subtle structural changes in the G4 structure upon ligand binding, molecular dynamics (MD) simulations of c-MYC G4 DNA were carried out in a complex with six different potent ligands: 3AQN, 6AQN, 3APN, 360A, Nap-Et, and Nap-Pr. The results show that the ligands 3AQN, 6AQN, 3APN, and 360A stabilize the G4 structure by making stacking interactions with the top quartet. On the other hand, Nap-Et and Nap-Pr bind at the groove of the G4 structure. These groove binding ligands make crucial H-bond contacts with the guanines and electrostatic interactions with the phosphate backbone. Two-dimensional dynamic correlation maps unraveled the ligand-induced correlated motions between the guanines in the quartet and a di-nucleotide present in the propeller loop-2 of the G4 structure. Cluster analysis and ONIOM calculations revealed the structural dynamics in the loop of the quadruplex upon ligand binding. Overall, the results from the present study suggest that engineering specific contacts with the propeller loop can be an efficient way to design c-MYC G4-specific ligands.
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Affiliation(s)
- S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai - 400076, India.
| | - Saikiran Kotaru
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai - 400076, India.
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai - 400076, India.
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72
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Yoshida W, Saikyo H, Nakabayashi K, Yoshioka H, Bay DH, Iida K, Kawai T, Hata K, Ikebukuro K, Nagasawa K, Karube I. Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand. Sci Rep 2018; 8:3116. [PMID: 29449667 PMCID: PMC5814564 DOI: 10.1038/s41598-018-21514-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 02/05/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex (G4) is a DNA secondary structure that has been found to play regulatory roles in the genome. The identification of G4-forming sequences is important to study the specific structure-function relationships of such regions. In the present study, we developed a method for identification of G4 clusters on genomic DNA by high-throughput sequencing of genomic DNA amplified via whole-genome amplification (WGA) in the presence of a G4 ligand. The G4 ligand specifically bound to G4 structures on genomic DNA; thus, DNA polymerase was arrested on the G4 structures stabilised by G4 ligand. We utilised the telomestatin derivative L1H1-7OTD as a G4 ligand and demonstrated that the efficiency of amplification of the G4 cluster regions was lower than that of the non-G4-forming regions. By high-throughput sequencing of the WGA products, 9,651 G4 clusters were identified on human genomic DNA. Among these clusters, 3,766 G4 clusters contained at least one transcriptional start site, suggesting that genes are regulated by G4 clusters rather than by one G4 structure.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.
| | - Hiroki Saikyo
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
| | - Keisuke Iida
- Molecular Chirality Research Center, Synthetic Organic Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba, 263-8522, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
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73
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Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure. Sci Rep 2018; 8:2666. [PMID: 29422637 PMCID: PMC5805748 DOI: 10.1038/s41598-018-20960-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/26/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.
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74
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Tucker BA, Hudson JS, Ding L, Lewis E, Sheardy RD, Kharlampieva E, Graves D. Stability of the Na + Form of the Human Telomeric G-Quadruplex: Role of Adenines in Stabilizing G-Quadruplex Structure. ACS OMEGA 2018; 3:844-855. [PMID: 30023791 PMCID: PMC6045420 DOI: 10.1021/acsomega.7b01649] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/09/2018] [Indexed: 06/08/2023]
Abstract
G-quadruplexes are higher order DNA structures that play significant roles in gene transcription and telomeric maintenance. The formation and stability of the G-quadruplex structures are under thermodynamic control and may be of biological significance for regulatory function of cellular processes. Here, we report the structural influence and energetic contributions of the adenine bases in the loop sequences that flank G-repeats in human telomeric DNA sequence. Spectroscopic and calorimetric techniques are used to measure the thermal stability and thermodynamic contributions to the stability of human telomeric G-quadruplexes that have been designed with systematic changes of A to T throughout the telomeric sequence. These studies demonstrate that the thermal stability of the G-quadruplex structure is directly related to the number and position of the adenines that are present in the telomeric sequence. The melting temperature (Tm) was reduced from 59 °C for the wild-type sequence to 47 °C for the sequence where all four adenines were replaced with thymines (0123TTT). Furthermore, the enthalpy required for transitioning from the folded to unfolded G-quadruplex structure was reduced by 15 kcal/mol when the adenines were replaced with thymines (37 kcal/mol for the wild-type telomeric sequence reduced to 22 kcal/mol for the sequence where all four adenines were replaced with thymines (0123TTT)). The circular dichroism melting studies for G-quadruplex sequences having a single A to T change showed significantly sloping pretransition baselines and their differential scanning calorimetry (DSC) thermograms revealed biphasic melting profiles. In contrast, the deoxyoligonucleotides having sequences with two or more A to T changes did not exhibit sloping baselines or biphasic DSC thermograms. We attribute the biphasic unfolding profile and reduction in the enthalpy of unfolding to the energetic contributions of adenine hydrogen bonding within the loops as well as the adenine stacking to the G-tetrads of the G-quadruplex structure.
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Affiliation(s)
- Brenna A. Tucker
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Jason S. Hudson
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Lei Ding
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Edwin Lewis
- Department
of Chemistry, Mississippi State University, Mississippi, Mississippi
State 39762, United
States
| | - Richard D. Sheardy
- Department
of Chemistry & Biochemistry, Texas Women’s
University, Denton, Texas 782042, United States
| | - Eugenia Kharlampieva
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - David Graves
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
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75
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van Wietmarschen N, Merzouk S, Halsema N, Spierings DCJ, Guryev V, Lansdorp PM. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat Commun 2018; 9:271. [PMID: 29348659 PMCID: PMC5773480 DOI: 10.1038/s41467-017-02760-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022] Open
Abstract
Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing (Strand-seq) to map the genomic locations of SCEs. Our results show that in the absence of BLM, SCEs in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of guanine quadruplex (G4) motifs in transcribed genes. We propose that BLM protects against genome instability by suppressing recombination at sites of G4 structures, particularly in transcribed regions of the genome. Bloom syndrome is characterized by high levels of sister chromatid exchanges (SCEs). Here, the authors use single-cell DNA template strand-sequencing to map SCEs in patient cells, and propose that the BLM helicase protects the genome against unwanted recombination at sites of G-quadruplex structures.
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Affiliation(s)
- Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sarra Merzouk
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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76
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Yangyuoru PM, Bradburn DA, Liu Z, Xiao TS, Russell R. The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism. J Biol Chem 2017; 293:1924-1932. [PMID: 29269411 DOI: 10.1074/jbc.m117.815076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
Single-stranded DNA (ssDNA) and RNA regions that include at least four closely spaced runs of three or more consecutive guanosines strongly tend to fold into stable G-quadruplexes (G4s). G4s play key roles as DNA regulatory sites and as kinetic traps that can inhibit biological processes, but how G4s are regulated in cells remains largely unknown. Here, we developed a kinetic framework for G4 disruption by DEAH-box helicase 36 (DHX36), the dominant G4 resolvase in human cells. Using tetramolecular DNA and RNA G4s with four to six G-quartets, we found that DHX36-mediated disruption is highly efficient, with rates that depend on G4 length under saturating conditions (kcat) but not under subsaturating conditions (kcat/Km ). These results suggest that a step during G4 disruption limits the kcat value and that DHX36 binding limits kcat/Km Similar results were obtained for unimolecular DNA G4s. DHX36 activity depended on a 3' ssDNA extension and was blocked by a polyethylene glycol linker, indicating that DHX36 loads onto the extension and translocates 3'-5' toward the G4. DHX36 unwound dsDNA poorly compared with G4s of comparable intrinsic lifetime. Interestingly, we observed that DHX36 has striking 3'-extension sequence preferences that differ for G4 disruption and dsDNA unwinding, most likely arising from differences in the rate-limiting step for the two activities. Our results indicate that DHX36 disrupts G4s with a conventional helicase mechanism that is tuned for great efficiency and specificity for G4s. The dependence of DHX36 on the 3'-extension sequence suggests that the extent of formation of genomic G4s may not track directly with G4 stability.
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Affiliation(s)
- Philip M Yangyuoru
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
| | - Devin A Bradburn
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
| | - Zhonghua Liu
- the Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Tsan Sam Xiao
- the Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Rick Russell
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
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77
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Huang H, Zhang J, Harvey SE, Hu X, Cheng C. RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF. Genes Dev 2017; 31:2296-2309. [PMID: 29269483 PMCID: PMC5769772 DOI: 10.1101/gad.305862.117] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022]
Abstract
Here, Huang et al. investigated the role of RNA secondary structure in splicing regulation and show that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in hnRNPF-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome, thus providing new insights into the regulation of alternative splicing. It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Destroying G-quadruplex-forming capacity while keeping G tracts intact abrogates exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in heterogeneous nuclear ribonucleoprotein F (hnRNPF)-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome. Moreover, hnRNPF regulates an epithelial–mesenchymal transition (EMT)-associated CD44 isoform switch in a G-quadruplex-dependent manner, which results in inhibition of EMT. Mining breast cancer TCGA (The Cancer Genome Atlas) data sets, we demonstrate that hnRNPF negatively correlates with an EMT gene signature and positively correlates with patient survival. These data suggest a critical role for RNA G quadruplexes in regulating alternative splicing. Modulation of G-quadruplex structural integrity may control cellular processes important for tumor progression.
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Affiliation(s)
- Huilin Huang
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jing Zhang
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Samuel E Harvey
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaohui Hu
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chonghui Cheng
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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78
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Wang S, Lu S, Zhao J, Huang J, Yang X. Real-Time Study of the Interaction between G-Rich DNA Oligonucleotides and Lead Ion on DNA Tetrahedron-Functionalized Sensing Platform by Dual Polarization Interferometry. ACS APPLIED MATERIALS & INTERFACES 2017; 9:41568-41576. [PMID: 29099169 DOI: 10.1021/acsami.7b13477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb2+. The oriented immobilization of probes greatly decreased the spatial hindrance effect and improved the accessibility of the probes to the Pb2+ ions. Through real-time monitoring of the whole formation process of the G-quadruplex, we speculated that the probes on the tetrahedron platform initially stood on the sensing surface with a random coil conformation, then the G-rich ssDNA preliminarily formed unstable G-quartets by H-bonding and cation binding, subsequently forming a completely folded and stable quadruplex structure through relatively slow strand rearrangements. On the basis of these studies, we also developed a novel sensing platform for the specific and sensitive determination of Pb2+ and its chelating agent ethylenediaminetetraacetic acid. This study not only provides a proof-of-concept for conformational dynamics of G-quadruplex-related drugs and pathogenes, but also enriches the biosensor tools by combining nanomaterial with interfaces technique.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100039, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Changchun, Jilin 130022, China
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79
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Cammas A, Millevoi S. RNA G-quadruplexes: emerging mechanisms in disease. Nucleic Acids Res 2017; 45:1584-1595. [PMID: 28013268 PMCID: PMC5389700 DOI: 10.1093/nar/gkw1280] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022] Open
Abstract
RNA G-quadruplexes (G4s) are formed by G-rich RNA sequences in protein-coding (mRNA) and non-coding (ncRNA) transcripts that fold into a four-stranded conformation. Experimental studies and bioinformatic predictions support the view that these structures are involved in different cellular functions associated to both DNA processes (telomere elongation, recombination and transcription) and RNA post-transcriptional mechanisms (including pre-mRNA processing, mRNA turnover, targeting and translation). An increasing number of different diseases have been associated with the inappropriate regulation of RNA G4s exemplifying the potential importance of these structures on human health. Here, we review the different molecular mechanisms underlying the link between RNA G4s and human diseases by proposing several overlapping models of deregulation emerging from recent research, including (i) sequestration of RNA-binding proteins, (ii) aberrant expression or localization of RNA G4-binding proteins, (iii) repeat associated non-AUG (RAN) translation, (iv) mRNA translational blockade and (v) disabling of protein–RNA G4 complexes. This review also provides a comprehensive survey of the functional RNA G4 and their mechanisms of action. Finally, we highlight future directions for research aimed at improving our understanding on RNA G4-mediated regulatory mechanisms linked to diseases.
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Affiliation(s)
- Anne Cammas
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III-Paul Sabatier, Inserm, CRCT, Toulouse, France
| | - Stefania Millevoi
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III-Paul Sabatier, Inserm, CRCT, Toulouse, France
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80
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Kazemier HG, Paeschke K, Lansdorp PM. Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA. Nucleic Acids Res 2017; 45:5913-5919. [PMID: 28449085 PMCID: PMC5449594 DOI: 10.1093/nar/gkx245] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/04/2017] [Indexed: 01/09/2023] Open
Abstract
Previously we reported the production and characterization of monoclonal antibody 1H6 raised against (T4G4)2 intermolecular guanine quadruplex (G4) DNA structures (Henderson A. et al. (2014) Nucleic Acids Res., 42, 860–869; Hoffmann R.F. et al. (2016) Nucleic Acids Res., 44, 152–163). It was shown that 1H6 strongly stains nuclei and has exquisite specificity for heterochromatin by immuno-electron microscopy. Here we extend our studies of 1H6 reactivity using enzyme-linked immunosorbent assay (ELISA) and microscale thermophoresis (MST). As previously reported, 1H6 was found to strongly bind intermolecular G4 structures with a (T4G4)2 sequence motif. However, using both methods we did not detect significant binding to G4 structures without thymidines in their sequence motif or to G4 structures made with (T2G4)2 oligonucleotides. In addition, we observed strong, sequence-specific binding of 1H6 by ELISA to immobilized single stranded poly(T) DNA but not to immobilized poly(C) or poly(A) homo-polymers. Cross-reactivity of 1H6 to poly(T) was not measured in solution using MST. 1H6 was furthermore found to bind to selected areas on DNA fibers but only after DNA denaturation. Based on these observations we propose that 1H6 binds with high affinity to adjacent T's that are restricted in their movement in selected G4 structures and denatured DNA. Cross-reactivity of 1H6 to immobilized single stranded T-rich DNA next to its previously reported specificity for bona fide G4 structures needs to be taken into account in the interpretation of 1H6 binding to (sub-) cellular structures.
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Affiliation(s)
- Hinke G Kazemier
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Katrin Paeschke
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.,Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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81
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Adrian M, Winnerdy FR, Heddi B, Phan AT. Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding. Biophys J 2017; 113:775-784. [PMID: 28834714 DOI: 10.1016/j.bpj.2017.05.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/25/2022] Open
Abstract
Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.
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Affiliation(s)
- Michael Adrian
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Brahim Heddi
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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82
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83
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Bay DH, Busch A, Lisdat F, Iida K, Ikebukuro K, Nagasawa K, Karube I, Yoshida W. Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands. BMC Mol Biol 2017; 18:17. [PMID: 28655335 PMCID: PMC5488298 DOI: 10.1186/s12867-017-0094-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/23/2017] [Indexed: 12/29/2022] Open
Abstract
Background G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay. Results When G-quadruplex-forming sequences from the Dele and Cdc6 genes have been cloned in reporter vectors carrying a minimal promoter and the luciferase gene, luciferase expression is activated. This has also been detected in experiments applying a promoterless reporter vector. Mutational analysis reveals that guanine bases, which form the G-tetrads, are important in the activation. In addition, the activation has been found to decrease by the telomestatin derivative L1H1-7OTD which can bind to the G-quadruplex DNA. When Dele and Cdc6 CpG islands, containing the G-quadruplex-forming sequence, have been cloned in the promoterless reporter vector, the luciferase expression is activated. Mutational analysis reveals that the expression level is decreased by mutation on Dele G-quadruplex; however, increased by mutation on Cdc6 G-quadruplex. Conclusion Dele and Cdc6 G-quadruplex formation is significant in the transcriptional regulation. Dele and Cdc6 G-quadruplex DNA alone possess enhancer and promotor function. When studied in more complex CpG islands Dele G-quadruplex also demonstrates promotor activity, whereas Cdc6 G-quadruplex may possess a dual function of transcriptional regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0094-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniyah H Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Annika Busch
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Fred Lisdat
- Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University, c/o Saitama Cancer Center, Saitama, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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84
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Soemedi R, Cygan KJ, Rhine CL, Glidden DT, Taggart AJ, Lin CL, Fredericks AM, Fairbrother WG. The effects of structure on pre-mRNA processing and stability. Methods 2017; 125:36-44. [PMID: 28595983 DOI: 10.1016/j.ymeth.2017.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and various algorithms that use minimum free energy, maximum expected accuracy and comparative evolutionary based methods have been developed to predict secondary structures. However, these tools are not perfect, and this remains an active area of research. The secondary structure of pre-mRNA molecules can have an enhancing or inhibitory effect on pre-mRNA splicing. An example of enhancing structure can be found in a novel class of introns in zebrafish. About 10% of zebrafish genes contain a structured intron that forms a bridging hairpin that enforces correct splice site pairing. Negative examples of splicing include local structures around splice sites that decrease splicing efficiency and potentially cause mis-splicing leading to disease. Splicing mutations are a frequent cause of hereditary disease. The transcripts of disease genes are significantly more structured around the splice sites, and point mutations that increase the local structure often cause splicing disruptions. Post-splicing, RNA secondary structure can also affect the stability of the spliced intron and regulatory RNA interference pathway intermediates, such as pre-microRNAs. Additionally, RNA secondary structure has important roles in the innate immune defense against viruses. Finally, tertiary structure can also play a large role in pre-mRNA splicing. One example is the G-quadruplex structure, which, similar to secondary structure, can either enhance or inhibit splicing through mechanisms such as creating or obscuring RNA binding protein sites.
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Affiliation(s)
- Rachel Soemedi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Kamil J Cygan
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Christy L Rhine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - David T Glidden
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - Chien-Ling Lin
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - Alger M Fredericks
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
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85
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Varizhuk A, Ischenko D, Tsvetkov V, Novikov R, Kulemin N, Kaluzhny D, Vlasenok M, Naumov V, Smirnov I, Pozmogova G. The expanding repertoire of G4 DNA structures. Biochimie 2017; 135:54-62. [PMID: 28109719 DOI: 10.1016/j.biochi.2017.01.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/30/2016] [Accepted: 01/12/2017] [Indexed: 11/17/2022]
Abstract
The definition of DNA and RNA G-quadruplexes (G4s) has recently been broadened to include structures with certain defects: bulges, G-vacancies or mismatches. Despite the striking progress in computational methods for assessing G4 folding propensity, predicting G4s with defects remains problematic, reflecting the enhanced sequential diversity of these motifs. "Imperfect" G4 motifs, i.e., those containing interrupted or truncated G-runs, are typically omitted from genomic analyses. We report here studies of G4s with defects and compare these structures with classical ("perfect") quadruplexes. Thermal stabilities and ligand interactions are also discussed. We exploited a simple in-house computational tool for mining putative G4s with defects in the human genome. The obtained profiles of the genomic distribution of imperfect G4 motifs were analyzed. Collectively, our findings suggest that, similar to classical G4s, imperfect G4s could be considered as potential regulatory elements, pathology biomarkers and therapeutic targets.
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Affiliation(s)
- Anna Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Engenlhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - Dmitry Ischenko
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Moscow Institute of Physics and Technology (State University), 117303 Moscow, Russia
| | - Vladimir Tsvetkov
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of the Russian Federation, Saint Petersburg, Russia
| | - Roman Novikov
- Engenlhardt Institute of Molecular Biology, 119991 Moscow, Russia; N.D. Zelinsky Institute of Organic Chemistry, Moscow 119991, Russia
| | - Nikolay Kulemin
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Moscow Institute of Physics and Technology (State University), 117303 Moscow, Russia
| | - Dmitry Kaluzhny
- Engenlhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - Maria Vlasenok
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Moscow Institute of Physics and Technology (State University), 117303 Moscow, Russia
| | - Vladimir Naumov
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia
| | - Igor Smirnov
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia
| | - Galina Pozmogova
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia.
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86
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Shioda N. [Involvement of G-quadruplexes in neurodegenerative diseases]. Nihon Yakurigaku Zasshi 2017; 150:298. [PMID: 29225293 DOI: 10.1254/fpj.150.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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87
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Kaplan OI, Berber B, Hekim N, Doluca O. G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch. Nucleic Acids Res 2016; 44:9083-9095. [PMID: 27596596 PMCID: PMC5100583 DOI: 10.1093/nar/gkw769] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.
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Affiliation(s)
- Oktay I Kaplan
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, 13125 Berlin, Germany
- School of Medicine, Istanbul Medeniyet University, 34000 Istanbul, Turkey
| | - Burak Berber
- Department of Biology, Osmangazi University, Eskisehir, 26480, Turkey
| | - Nezih Hekim
- School of Medicine, Istanbul Kemerburgaz University, 34217, Turkey
| | - Osman Doluca
- Department of Biomedical Engineering, Izmir University of Economics, Izmir, 35330, Turkey
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88
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Doria F, Nadai M, Costa G, Sattin G, Gallati C, Bergamaschi G, Moraca F, Alcaro S, Freccero M, Richter SN. Extended Naphthalene Diimides with Donor/Acceptor Hydrogen-Bonding Properties Targeting G-Quadruplex Nucleic Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Filippo Doria
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Matteo Nadai
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Giovanna Sattin
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
| | - Caroline Gallati
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Greta Bergamaschi
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Mauro Freccero
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Sara N. Richter
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
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89
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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90
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Richard P, Manley JL. R Loops and Links to Human Disease. J Mol Biol 2016; 429:3168-3180. [PMID: 27600412 DOI: 10.1016/j.jmb.2016.08.031] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022]
Abstract
Aberrant R-loop structures are increasingly being realized as an important contributor to human disease. R loops, which are mainly co-transcriptional, abundant RNA/DNA hybrids, form naturally and can indeed be beneficial for transcription regulation at certain loci. However, their unwanted persistence elsewhere or in particular situations can lead to DNA double-strand breaks, chromosome rearrangements, and hypermutation, which are all sources of genomic instability. Mutations in genes involved in R-loop resolution or mutations leading to R-loop formation at specific genes affect the normal physiology of the cell. We discuss here the examples of diseases for which a link with R loops has been described, as well as how disease-causing mutations might participate in the development and/or progression of diseases that include repeat-associated conditions, other neurological disorders, and cancers.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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91
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De Nicola B, Lech CJ, Heddi B, Regmi S, Frasson I, Perrone R, Richter SN, Phan AT. Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome. Nucleic Acids Res 2016; 44:6442-51. [PMID: 27298260 PMCID: PMC5291261 DOI: 10.1093/nar/gkw432] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
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Affiliation(s)
- Beatrice De Nicola
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore Department of Molecular Medicine, University of Padua, Italy
| | - Christopher J Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Sagar Regmi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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92
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Costa G, Rocca R, Moraca F, Talarico C, Romeo I, Ortuso F, Alcaro S, Artese A. A Comparative Docking Strategy to Identify Polyphenolic Derivatives as Promising Antineoplastic Binders of G-quadruplex DNAc-mycandbcl-2Sequences. Mol Inform 2016; 35:391-402. [DOI: 10.1002/minf.201501040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/19/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Giosuè Costa
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Roberta Rocca
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Federica Moraca
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Carmine Talarico
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Isabella Romeo
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Francesco Ortuso
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Stefano Alcaro
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
| | - Anna Artese
- Università degli Studi “Magna Graecia” di Catanzaro, Dipartimento di Scienze della Salute; Campus “Salvatore Venuta”, Viale Europa 88100 Catanzaro Italy
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93
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Zhao A, Zhao C, Tateishi-Karimata H, Ren J, Sugimoto N, Qu X. Incorporation of O(6)-methylguanine restricts the conformational conversion of the human telomere G-quadruplex under molecular crowding conditions. Chem Commun (Camb) 2016; 52:1903-6. [PMID: 26673900 DOI: 10.1039/c5cc09728b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here we systematically studied the incorporation of O(6)-methylguanine (6mG) into different positions of the human telomere G-quadruplex. In contrast to the natural G-quadruplex, the 6mG incorporated G-quadruplexes impeded the conformational conversion of the G-quadruplex from a hybrid to a parallel structure under molecular crowding conditions in a K(+) containing buffer.
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Affiliation(s)
- Andong Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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94
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Diveshkumar KV, Sakrikar S, Rosu F, Harikrishna S, Gabelica V, Pradeepkumar PI. Specific Stabilization of c-MYC and c-KIT G-Quadruplex DNA Structures by Indolylmethyleneindanone Scaffolds. Biochemistry 2016; 55:3571-85. [DOI: 10.1021/acs.biochem.6b00120] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. V. Diveshkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Saaz Sakrikar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Frédéric Rosu
- CNRS, UMS3033/US001,
Institut Européen de Chimie et Biologie, 33607 Pessac, France
- Université
de Bordeaux, U869 ARNA Laboratory, 33600 Pessac, France
| | - S. Harikrishna
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Valérie Gabelica
- Université
de Bordeaux, U869 ARNA Laboratory, 33600 Pessac, France
- Inserm, U869 ARNA
Laboratory, 33000 Bordeaux, France
| | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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95
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González C, Salces-Ortiz J, Calvo JH, Serrano MM. In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene. Cell Stress Chaperones 2016; 21:415-27. [PMID: 26810179 PMCID: PMC4837184 DOI: 10.1007/s12192-016-0668-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/02/2016] [Accepted: 01/06/2016] [Indexed: 01/21/2023] Open
Abstract
Gene promoters are essential regions of DNA where the transcriptional molecular machinery to produce RNA molecules is recruited. In this process, DNA epigenetic modifications can acquire a fundamental role in the regulation of gene expression. Recently, in a previous work of our group, functional features and DNA methylation involved in the ovine HSP90AA1 gene expression regulation have been observed. In this work, we report a combination of methylation analysis by bisulfite sequencing in several tissues and at different developmental stages together with in silico bioinformatic analysis of putative regulating factors in order to identify regulative mechanisms both at the promoter and gene body. Our results show a "hybrid structure" (TATA box + CpG island) of the ovine HSP90AA1 gene promoter both in somatic and non-differentiated germ tissues, revealing the ability of the HSP90AA1 gene to be regulated both in an inducible and constitutive fashion. In addition, in silico analysis showed that several putative alternative spliced regulatory motifs, exonic splicing enhancers (ESEs), and G-quadruplex secondary structures were somehow related to the DNA methylation pattern found. The results obtained here could help explain the differences in cell-type transcripts, tissue expression rate, and transcription silencing mechanisms found in this gene.
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Affiliation(s)
| | | | - Jorge H Calvo
- Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain
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96
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Lu YJ, Deng Q, Hou JQ, Hu DP, Wang ZY, Zhang K, Luyt LG, Wong WL, Chow CF. Molecular Engineering of Thiazole Orange Dye: Change of Fluorescent Signaling from Universal to Specific upon Binding with Nucleic Acids in Bioassay. ACS Chem Biol 2016; 11:1019-29. [PMID: 26752011 DOI: 10.1021/acschembio.5b00987] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The universal fluorescent staining property of thiazole orange (TO) dye was adapted in order to be specific for G-quadruplex DNA structures, through the introduction of a styrene-like substituent at the ortho-position of the TO scaffold. This extraordinary outcome was determined from experimental studies and further explored through molecular docking studies. The molecular docking studies help understand how such a small substituent leads to remarkable fluorescent signal discrimination between G-quadruplex DNA and other types of nucleic acids. The results reveal that the modified dyes bind to the G-quadruplex or duplex DNA in a similar fashion as TO, but exhibit either enhanced or quenched fluorescent signal, which is determined by the spatial length and orientation of the substituent and has never been known. The new fluorescent dye modified with a p-(dimethylamino)styryl substituent offers 10-fold more selectivity toward telomeric G-quadruplexes than double-stranded DNA substrates. In addition, native PAGE experiments, FRET, CD analysis, and live cell imaging were also studied and demonstrated the potential applications of this class of thiazole-orange-based fluorescent probes in bioassays and cell imaging.
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Affiliation(s)
- Yu-Jing Lu
- Institute
of Natural Medicine and Green Chemistry, School of Chemical Engineering
and Light Industry, Guangdong University of Technology, Guangzhou 510006, Peoples’ Republic of China
| | - Qiang Deng
- Institute
of Natural Medicine and Green Chemistry, School of Chemical Engineering
and Light Industry, Guangdong University of Technology, Guangzhou 510006, Peoples’ Republic of China
| | - Jin-Qiang Hou
- London Regional Cancer Program, 790 Commissioners Road East, London, Ontario N6A 4L6, Canada
| | - Dong-Ping Hu
- Institute
of Natural Medicine and Green Chemistry, School of Chemical Engineering
and Light Industry, Guangdong University of Technology, Guangzhou 510006, Peoples’ Republic of China
| | - Zheng-Ya Wang
- Institute
of Natural Medicine and Green Chemistry, School of Chemical Engineering
and Light Industry, Guangdong University of Technology, Guangzhou 510006, Peoples’ Republic of China
| | - Kun Zhang
- Institute
of Natural Medicine and Green Chemistry, School of Chemical Engineering
and Light Industry, Guangdong University of Technology, Guangzhou 510006, Peoples’ Republic of China
| | - Leonard G. Luyt
- London Regional Cancer Program, 790 Commissioners Road East, London, Ontario N6A 4L6, Canada
- Departments
of Oncology, Chemistry, Medical Imaging, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Wing-Leung Wong
- Department
of Science and Environmental Studies, Centre for Education in Environmental
Sustainability, The Hong Kong Institute of Education, 10 Lo Ping
Road, Tai Po, Hong Kong SAR, Peoples’ Republic of China
| | - Cheuk-Fai Chow
- Department
of Science and Environmental Studies, Centre for Education in Environmental
Sustainability, The Hong Kong Institute of Education, 10 Lo Ping
Road, Tai Po, Hong Kong SAR, Peoples’ Republic of China
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97
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Oyaghire SN, Cherubim CJ, Telmer CA, Martinez JA, Bruchez MP, Armitage BA. RNA G-Quadruplex Invasion and Translation Inhibition by Antisense γ-Peptide Nucleic Acid Oligomers. Biochemistry 2016; 55:1977-88. [PMID: 26959335 DOI: 10.1021/acs.biochem.6b00055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the abilities of three complementary γ-peptide nucleic acid (γPNA) oligomers to invade an RNA G-quadruplex and potently inhibit translation of a luciferase reporter transcript containing the quadruplex-forming sequence (QFS) within its 5'-untranslated region. All three γPNA oligomers bind with low nanomolar affinities to an RNA oligonucleotide containing the QFS. However, while all probes inhibit translation with low to midnanomolar IC50 values, the γPNA designed to hybridize to the first two G-tracts of the QFS and adjacent 5'-overhanging nucleotides was 5-6 times more potent than probes directed to either the 3'-end or internal regions of the target at 37 °C. This position-dependent effect was eliminated after the probes and target were preincubated at an elevated temperature prior to translation, demonstrating that kinetic effects exert significant control over quadruplex invasion and translation inhibition. We also found that antisense γPNAs exhibited similarly potent effects against luciferase reporter transcripts bearing QFS motifs having G2, G3, or G4 tracts. Finally, our results indicate that γPNA oligomers exhibit selectivity and/or potency higher than those of other antisense molecules such as standard PNA and 2'-OMe RNA previously reported to target G-quadruplexes in RNA.
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Affiliation(s)
- Stanley N Oyaghire
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Collin J Cherubim
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Cheryl A Telmer
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Joe A Martinez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Marcel P Bruchez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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98
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Wu S, Wang L, Zhang N, Liu Y, Zheng W, Chang A, Wang F, Li S, Shangguan D. A Bis(methylpiperazinylstyryl)phenanthroline as a Fluorescent Ligand for G-Quadruplexes. Chemistry 2016; 22:6037-47. [PMID: 26990217 DOI: 10.1002/chem.201505170] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Indexed: 11/08/2022]
Abstract
G-quadruplex (G4)-forming sequences are prevalent in the genome and are considered to play important roles in gene regulation, and hence have been viewed as potential therapeutic targets in oncology. However, the structures and functions of most G4s in the genome are poorly understood. Therefore, the development of fluorescent probes and ligands for G4s is important for G4 research and drug discovery. Herein, we report a new G4 ligand, 2,9-bis[4-(4-methylpiperazin-1-yl)styryl]-1,10-phenanthroline (BMSP), which was synthesized by a simple process. BMSP exhibits almost no fluorescence in aqueous buffer. The interaction of BMSP with G4s greatly enhances its fluorescence with a large Stokes' shift of 160 nm. Antiparallel human telomeric G4s exhibit the strongest binding affinity (Kd ≈0.13 μm) to BMSP and induce a fluorescence enhancement of up to 150-fold. BMSP binds to G4s through π-π stacking on the terminal G-quartets. BMSP can enter live cells, and it strongly inhibits the growth of cancer cells rather than causing cell death. Our results suggest that BMSP has the potential to serve both as a fluorescent probe for some G4s and as a chemotherapeutic agent for cancer treatment.
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Affiliation(s)
- Shangrong Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509.,College of Chemistry, Xiangtan University, Xiangtan, 411100, China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Wei Zheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Ang Chang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509.,College of Chemistry, Xiangtan University, Xiangtan, 411100, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Songqin Li
- College of Chemistry, Xiangtan University, Xiangtan, 411100, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509.
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99
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Kogut M, Kleist C, Czub J. Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad-a common structural unit of G-quadruplex DNA. Nucleic Acids Res 2016; 44:3020-30. [PMID: 26980278 PMCID: PMC4838382 DOI: 10.1093/nar/gkw160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/01/2016] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully understood at the molecular level. Here, we used all-atom molecular dynamics to probe the microscopic origin of the G4 motif stability. By computing the free energy profiles governing the dissociation of the 3′-terminal G-tetrad in the telomeric parallel-stranded G4, we examined the thermodynamic and kinetic stability of a single G-tetrad, as a common structural unit of G4 DNA. Our results indicate that the energetics of guanine association alone does not explain the overall stability of the G-tetrad and that interactions involving sugar–phosphate backbone, in particular, the constrained minimization of the phosphate–phosphate repulsion energy, are crucial in providing the observed enthalpic stabilization. This enthalpic gain is largely compensated by the unfavorable entropy change due to guanine association and optimization of the backbone topology.
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Affiliation(s)
- Mateusz Kogut
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Cyprian Kleist
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
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100
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New pyridinium-based fluorescent dyes: A comparison of symmetry and side-group effects on G-Quadruplex DNA binding selectivity and application in live cell imaging. Biosens Bioelectron 2016; 81:373-381. [PMID: 26994364 DOI: 10.1016/j.bios.2016.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022]
Abstract
A series of C1-, C2-and C3-symmetric pyridinium conjugates with different styrene-like side groups were synthesized and were utilized as G-quadruplex selective fluorescent probes. The new compounds were well-characterized. Their selectivity, sensitivity, and stability towards G-quadruplex were studied by fluorescence titration, native PAGE experiments, FRET and circular dichroism (CD) analyses. These new compounds investigated in the fluorescence assays were preferentially bound with G-quadruplex DNA compared with other type of nucleic acids and it is fascinating to realize the effects of molecular symmetry and associated side groups showing unexpectedly great influence on the fluorescent signal enhancement for the discrimination of G-quadruplexes DNA from other nucleic acids. This may correlate with the pocket symmetry and shape of the G-quadruplex DNA inherently. Among the compounds, a C2-symmetric dye (2,6-bis-((E)-2-(1H-indol-3-yl)-vinyl)-1-methylpyridin-1-ium iodide) with indolyl-groups substituted was screened out from the series giving the best selectivity and sensitivity towards G-quadruplexes DNA, particularly telo21, due to its high equilibrium binding constant (K=2.17×10(5)M(-1)). In addition, the limit of detection (LOD) of the dye to determine telo21 DNA in bioassays was found as low as 33nM. The results of the study give insight and certain crucial factors, such as molecular symmetry and the associated side groups, on developing of effective fluorescent dyes for G-quadruplex DNA applications including G-quadruplex structure stabilization, biosensing and clinical applications. The compound was also demonstrated as a very selective G-quadruplex fluorescent agent for living cell staining and imaging.
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