1
|
Liang HT, Yan JY, Yao HJ, Zhang XN, Xing ZM, Liu L, Chen YQ, Li GR, Huang J, He YD, Zheng KW. G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity. Nucleic Acids Res 2024; 52:2142-2156. [PMID: 38340342 PMCID: PMC10954455 DOI: 10.1093/nar/gkae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/03/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1-G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.
Collapse
Affiliation(s)
- Hui-ting Liang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jiang-yu Yan
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Hao-jun Yao
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Xue-nan Zhang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Zhi-ming Xing
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yao-qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Guo-rui Li
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Huang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Yi-de He
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Ke-wei Zheng
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| |
Collapse
|
2
|
Lista MJ, Jousset AC, Cheng M, Saint-André V, Perrot E, Rodrigues M, Di Primo C, Gadelle D, Toccafondi E, Segeral E, Berlioz-Torrent C, Emiliani S, Mergny JL, Lavigne M. DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence. Retrovirology 2023; 20:10. [PMID: 37254203 DOI: 10.1186/s12977-023-00625-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/20/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Once integrated in the genome of infected cells, HIV-1 provirus is transcribed by the cellular transcription machinery. This process is regulated by both viral and cellular factors, which are necessary for an efficient viral replication as well as for the setting up of viral latency, leading to a repressed transcription of the integrated provirus. RESULTS In this study, we examined the role of two parameters in HIV-1 LTR promoter activity. We identified DNA topoisomerase1 (TOP1) to be a potent repressor of this promoter and linked this repression to its catalytic domain. Additionally, we confirmed the folding of a Guanine quadruplex (G4) structure in the HIV-1 promoter and its repressive effect. We demonstrated a direct interaction between TOP1 and this G4 structure, providing evidence of a functional relationship between the two repressive elements. Mutations abolishing G4 folding affected TOP1/G4 interaction and hindered G4-dependent inhibition of TOP1 catalytic activity in vitro. As a result, HIV-1 promoter activity was reactivated in a native chromatin environment. Lastly, we noticed an enrichment of predicted G4 sequences in the promoter of TOP1-repressed cellular genes. CONCLUSIONS Our results demonstrate the formation of a TOP1/G4 complex on the HIV-1 LTR promoter and its repressive effect on the promoter activity. They reveal the existence of a new mechanism of TOP1/G4-dependent transcriptional repression conserved between viral and human genes. This mechanism contrasts with the known property of TOP1 as global transcriptional activator and offers new perspectives for anti-cancer and anti-viral strategies.
Collapse
Affiliation(s)
- María José Lista
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Anne-Caroline Jousset
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
- Université de Strasbourg, CNRS UPR 9002, Architecture et réactivité de l'ARN, 67000, Strasbourg, France
| | - Mingpan Cheng
- CNRS UMR 5320, INSERM U1212, ARNA, Univ. Bordeaux, IECB, 33000, Bordeaux, France
- School of Engineering, China Pharmaceutical University, Nanjing, 211198, China
| | - Violaine Saint-André
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, 75015, Paris, France
| | - Elouan Perrot
- Institut Pasteur, Departement of Virology, Université Paris Cité, 75015, Paris, France
| | - Melissa Rodrigues
- Institut Pasteur, Departement of Virology, Université Paris Cité, 75015, Paris, France
| | - Carmelo Di Primo
- CNRS UMR 5320, INSERM U1212, ARNA, Univ. Bordeaux, IECB, 33000, Bordeaux, France
| | - Danielle Gadelle
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif Sur Yvette, Cedex, France
| | - Elenia Toccafondi
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
- Université de Strasbourg, CNRS UPR 9002, Architecture et réactivité de l'ARN, 67000, Strasbourg, France
| | - Emmanuel Segeral
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | | | - Stéphane Emiliani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France
| | - Jean-Louis Mergny
- CNRS UMR 5320, INSERM U1212, ARNA, Univ. Bordeaux, IECB, 33000, Bordeaux, France
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Marc Lavigne
- Université Paris Cité, Institut Cochin, INSERM, CNRS, F-75014, Paris, France.
- Institut Pasteur, Departement of Virology, Université Paris Cité, 75015, Paris, France.
| |
Collapse
|
3
|
G4-interacting proteins endangering genomic stability at G4 DNA-forming sites. Biochem Soc Trans 2023; 51:403-413. [PMID: 36629511 PMCID: PMC10018705 DOI: 10.1042/bst20221018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
In guanine-rich DNA strands, base-base interactions among guanines allow the conformational shift from the B-form DNA to the non-canonical quadruplex or G4 structure. The functional significance of G4 DNA in vivo is largely dependent on the interaction with protein factors, many of which contain the arginine-glycine-glycine or RGG repeat and other consensus G4-binding motifs. These G4-interacting proteins can significantly modulate the effect of G4 DNA structure on genome maintenance, either preventing or aggravating G4-assoicated genome instability. While the role of helicases in resolving G4 DNA structure has been extensively discussed, identification and characterization of protein factors contributing to elevation in G4-associated genome instability has been relatively sparse. In this minireview, we will particularly highlight recent discoveries regarding how interaction between certain G4-binding proteins and G4 DNA could exacerbate genome instability potentiated by G4 DNA-forming sequences.
Collapse
|
4
|
Jo J, Bae S, Jeon J, Youn H, Lee G, Ban C. Bifunctional G-Quadruplex Aptamer Targeting Nucleolin and Topoisomerase 1: Antiproliferative Activity and Synergistic Effect of Conjugated Drugs. Bioconjug Chem 2023; 34:238-247. [PMID: 36516871 DOI: 10.1021/acs.bioconjchem.2c00540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As a counterpart to antibody-drug conjugates (ADCs), aptamer-drug conjugates (ApDCs) have been considered a promising strategy for targeted therapy due to the various benefits of aptamers. However, an aptamer merely serves as a targeting ligand in ApDCs, whereas the antibody enables the unexpected therapeutic efficacy of ADCs through antibody-dependent cellular cytotoxicity (ADCC). In this study, we developed a tumor-specific aptamer with an effector function and used it to confirm the feasibility of more potent ApDCs. First, we designed a nucleolin (NCL)-binding G-quadruplex (GQ) library based on the ability of NCL to bind to telomeric sequences. We then identified a bifunctional GQ aptamer (BGA) inhibiting the catalytic activity of topoisomerase 1 (TOP1) by forming an irreversible cleavage complex. Our BGA specifically targeted NCL-positive MCF-7 cells, exhibiting antiproliferative activity, and this suggested that tumor-specific therapeutic aptamers can be developed by using a biased library to screen aptamer candidates for functional targets. Finally, we utilized DM1, which has a synergistic interaction with TOP1 inhibitors, as a conjugated drug. BGA-DM1 exerted an anticancer effect 20-fold stronger than free DM1 and even 10-fold stronger than AS1411 (NCL aptamer)-DM1, highlighting our approach to develop synergistic ApDCs. Therefore, we anticipate that our library might be utilized for the identification of aptamers with effector functions. Furthermore, by employing such aptamers and appropriate drugs, synergistic ApDCs can be developed for targeted cancer therapy in a manner distinct from how ADCs exhibit additional therapeutic efficacy.
Collapse
Affiliation(s)
- Jihoon Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Sangmin Bae
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Jinseong Jeon
- POSTECH Biotech Center, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Gyeongjin Lee
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk790-784, Republic of Korea
| |
Collapse
|
5
|
Li D, Chen X, Yan R, Jiang Z, Zhou B, Lv B. G-quadruplex-containing oligodeoxynucleotides as DNA topoisomerase I inhibitors. Int J Biol Macromol 2022; 223:281-289. [PMID: 36356864 DOI: 10.1016/j.ijbiomac.2022.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
DNA topoisomerase I was found to be highly abundant in fast-proliferating tumor cells and is a potential target for anticancer therapy. A series of G-quadruplex-containing oligodeoxynucleotides (ODNs) were designed and used as inhibitors of DNA topoisomerase I. It was demonstrated that ODNs with G-quadruplexes can efficiently inhibit the supercoiled DNA relaxation reaction catalyzed by DNA topoisomerase I. Compared with the other conformations, the parallel propeller-type G-quadruplex was the most efficient DNA topoisomerase I inhibitor. Further studies revealed that integrating G-quadruplexes with duplexes to form quadruplex-duplex hybrids could significantly improve the inhibition efficiency. In addition, a circular ODN that consists of a G-quadruplex motif and DNA topoisomerase I binding site was synthesized and used as a DNA topoisomerase I inhibitor. The results showed that the particularly designed circular ODN displayed high inhibitory efficiency on the activity of DNA topoisomerase I with an IC50 value of 54.8 nM. Moreover, the circular ODN exhibited excellent thermal stability and nuclease resistance. Considering the low cytotoxicity of DNA-based biopharmaceuticals, the design strategy and results reported in this study may shed new light on nucleic acid-based DNA topoisomerase I inhibitor construction for potential anticancer drugs.
Collapse
Affiliation(s)
- Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Xiyu Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Rumeng Yan
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing 210013, China
| | - Zeshan Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Bing Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Bei Lv
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing 210013, China.
| |
Collapse
|
6
|
Amrane S, Jaubert C, Bedrat A, Rundstadler T, Recordon-Pinson P, Aknin C, Guédin A, De Rache A, Bartolucci L, Diene I, Lemoine F, Gascuel O, Pratviel G, Mergny JL, Andreola ML. Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection. Nucleic Acids Res 2022; 50:12328-12343. [PMID: 36453997 PMCID: PMC9757044 DOI: 10.1093/nar/gkac1030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/27/2022] [Accepted: 10/29/2022] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome. We identified 10 G4s with conservation rates higher than those of HIV-1 regulatory sequences such as RRE and TAR. We then used porphyrin-based G4-binders to probe the formation of the G4s during infection of human cells by native HIV-1. The G4-binders efficiently inhibited HIV-1 infectivity, which is attributed to the formation of G4 structures during HIV-1 replication. Using a qRT-PCR approach, we showed that the formation of viral G4s occurs during the first 2 h post-infection and their stabilization by the G4-binders prevents initiation of reverse transcription. We also used a G4-RNA pull-down approach, based on a G4-specific biotinylated probe, to allow the direct detection and identification of viral G4-RNA in infected cells. Most of the detected G4-RNAs contain crucial regulatory elements such as the PPT and cPPT sequences as well as the U3 region. Hence, these G4s would function in the early stages of infection when the viral RNA genome is being processed for the reverse transcription step.
Collapse
Affiliation(s)
- Samir Amrane
- To whom correspondence should be addressed. Tel : +33 5 4000 2224;
| | - Chloé Jaubert
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Amina Bedrat
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Tiffany Rundstadler
- Université de Toulouse, UPS, INPT, Toulouse, France,Laboratoire de Chimie de Coordination, CNRS UPR 8241, Toulouse, France
| | | | - Cindy Aknin
- Université de Bordeaux, Bordeaux, France,MFP laboratory, UMR5234, CNRS, Bordeaux, France
| | - Aurore Guédin
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Aurore De Rache
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Laura Bartolucci
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Ibra Diene
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Frédéric Lemoine
- Institut Pasteur, Université de Paris, Unité de Bioinformatique Évolutive, F-75015 Paris, France,Institut Pasteur, Université de Paris, Hub de bioinformatique et biostatistiques, F-75015 Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université de Paris, Unité de Bioinformatique Évolutive, F-75015 Paris, France,Institut de Systématique, Évolution, Biodiversité (ISYEB, UMR 7205 - CNRS, Muséum National d’Histoire Naturelle, SU, EPHE UA), F-75005 Paris, France
| | - Geneviève Pratviel
- Université de Toulouse, UPS, INPT, Toulouse, France,Laboratoire de Chimie de Coordination, CNRS UPR 8241, Toulouse, France
| | - Jean-Louis Mergny
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France,Laboratoire d’Optique & Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Marie-Line Andreola
- Université de Bordeaux, Bordeaux, France,MFP laboratory, UMR5234, CNRS, Bordeaux, France
| |
Collapse
|
7
|
Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. G-Quadruplex Structures in Bacteria: Functional Properties and Prospects for Use as Biotargets. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2022. [DOI: 10.1134/s1990750822040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
8
|
Miglietta G, Marinello J, Russo M, Capranico G. Ligands stimulating antitumour immunity as the next G-quadruplex challenge. Mol Cancer 2022; 21:180. [PMID: 36114513 PMCID: PMC9482198 DOI: 10.1186/s12943-022-01649-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractG-quadruplex (G4) binders have been investigated to discover new anticancer drugs worldwide in past decades. As these ligands are generally not highly cytotoxic, the discovery rational was mainly based on increasing the cell-killing potency. Nevertheless, no G4 binder has been shown yet to be effective in cancer patients. Here, G4 binder activity at low dosages will be discussed as a critical feature to discover ligands with therapeutic effects in cancer patients. Specific effects of G4 binders al low doses have been reported to occur in cancer and normal cells. Among them, genome instability and the stimulation of cytoplasmic processes related to autophagy and innate immune response open to the use of G4 binders as immune-stimulating agents. Thus, we propose a new rational of drug discovery, which is not based on cytotoxic potency but rather on immune gene activation at non-cytotoxic dosage.
Collapse
|
9
|
Keller JG, Hymøller KM, Thorsager ME, Hansen NY, Erlandsen JU, Tesauro C, Simonsen AKW, Andersen AB, VandsøPetersen K, Holm LL, Stougaard M, Andresen BS, Kristensen P, Frøhlich R, Knudsen BR. Topoisomerase 1 inhibits MYC promoter activity by inducing G-quadruplex formation. Nucleic Acids Res 2022; 50:6332-6342. [PMID: 35687110 PMCID: PMC9226537 DOI: 10.1093/nar/gkac482] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/28/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
We have investigated the function of human topoisomerase 1 (TOP1) in regulation of G-quadruplex (G4) formation in the Pu27 region of the MYC P1 promoter. Pu27 is among the best characterized G4 forming sequences in the human genome and it is well known that promoter activity is inhibited upon G4 formation in this region. We found that TOP1 downregulation stimulated transcription from a promoter with wildtype Pu27 but not if the G4 motif in Pu27 was interrupted by mutation(s). The effect was not specific to the MYC promoter and similar results were obtained for the G4 forming promoter element WT21. The other major DNA topoisomerases with relaxation activity, topoisomerases 2α and β, on the other hand, did not affect G4 dependent promoter activity. The cellular studies were supported by in vitro investigations demonstrating a high affinity of TOP1 for wildtype Pu27 but not for mutant sequences unable to form G4. Moreover, TOP1 was able to induce G4 formation in Pu27 inserted in double stranded plasmid DNA in vitro. This is the first time TOP1 has been demonstrated capable of inducing G4 formation in double stranded DNA and of influencing G4 formation in cells.
Collapse
Affiliation(s)
- Josephine Geertsen Keller
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | | | | | - Noriko Y Hansen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jens Uldum Erlandsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Anne Bech Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark.,Department of Pathology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.,Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Peter Kristensen
- Faculty of Engineering and Science, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| |
Collapse
|
10
|
Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
Collapse
Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| |
Collapse
|
11
|
Gao Z, Williams P, Li L, Wang Y. A Quantitative Proteomic Approach for the Identification of DNA Guanine Quadruplex-Binding Proteins. J Proteome Res 2021; 20:4919-4924. [PMID: 34570971 DOI: 10.1021/acs.jproteome.1c00603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA sequences of high guanine (G) content have the potential to form G quadruplex (G4) structures. A more complete understanding about the biological functions of G4 DNA requires the investigation about how these structures are recognized by proteins. Here, we conducted exhaustive quantitative proteomic experiments to profile the interaction proteomes of G4 structures by employing different sequences of G4 DNA derived from the human telomere and the promoters of c-MYC and c-KIT genes. Our results led to the identification of a number of candidate G4-interacting proteins, many of which were discovered here for the first time. These included three proteins that can bind to all three DNA G4 structures and 78 other proteins that can bind selectively to one or two of the three DNA G4 structure(s). We also validated that GRSF1 can bind directly and selectively toward G4 structure derived from the c-MYC promoter. Our quantitative proteomic screening also led to the identification of a number of candidate "antireader" proteins of G4 DNA. Together, we uncovered a number of cellular proteins that exhibit general and selective recognitions of G4 folding patterns, which underscore the complexity of G4 DNA in biology and the importance of understanding fully the G4-interaction proteome.
Collapse
Affiliation(s)
- Zi Gao
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Preston Williams
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| |
Collapse
|
12
|
Cheng Y, Zhang Y, You H. Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy. Biomolecules 2021; 11:1579. [PMID: 34827577 PMCID: PMC8615981 DOI: 10.3390/biom11111579] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force-spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.
Collapse
Affiliation(s)
| | | | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Y.C.); (Y.Z.)
| |
Collapse
|
13
|
Peng Y, Niu K, Yu G, Zheng M, Wei Q, Song Q, Feng Q. Identification of binding domains and key amino acids involved in the interaction between BmLARK and G4 structure in the BmPOUM2 promoter in Bombyx mori. INSECT SCIENCE 2021; 28:929-940. [PMID: 32496005 DOI: 10.1111/1744-7917.12831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/19/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
It has been found that the non-B form DNA structures, like G-quadruplex (G4) and i-motif, are involved in many important biological processes. Our previous study showed that the silkworm transcription factor BmLARK binds to the G4 structure in the promoter of the transcription factor BmPOUM2 and regulates its promoter activity. However, the binding mechanism between BmLARK and BmPOUM2 G4 structure remains unclear. In this study, binding domains and key amino acid residues involved in the interaction between BmLARK and BmPOUM2 G4 were studied. The electrophoretic mobility shift assay results indicated that the two RNA-recognition motifs (RRM) of BmLARK are simultaneously required for the binding with the G4 structure. Either RRM1 or RRM2 alone could not bind with the G4 structure. The zinc-finger motif was not involved in the binding. A series of mutant proteins with specific amino acid mutations were expressed and used to identify the key amino acid residues involving the interaction. The results indicated that β sheets, especially the β1 and β3 sheets, in the RRM domains of BmLARK played critical roles in the binding with the G4 structure. Several amino acid mutations of RRM1/2 in ribonucleoprotein domain 1 (RNP1) (motif in β3 strand) and RNP2 (motif in β1 strand) caused loss of binding ability, indicating that these amino acids are the key sites for the binding. All the results suggest that RRM domains, particularly their the RNP1 and RNP2 motifs, play important roles not only in RNA recognition, but also in the G4 structure binding.
Collapse
Affiliation(s)
- Yuling Peng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Kangkang Niu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Guoxing Yu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Mingxi Zheng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qiulan Wei
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| |
Collapse
|
14
|
Cristini A, Géraud M, Sordet O. Transcription-associated DNA breaks and cancer: A matter of DNA topology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:195-240. [PMID: 34507784 DOI: 10.1016/bs.ircmb.2021.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transcription is an essential cellular process but also a major threat to genome integrity. Transcription-associated DNA breaks are particularly detrimental as their defective repair can induce gene mutations and oncogenic chromosomal translocations, which are hallmarks of cancer. The past few years have revealed that transcriptional breaks mainly originate from DNA topological problems generated by the transcribing RNA polymerases. Defective removal of transcription-induced DNA torsional stress impacts on transcription itself and promotes secondary DNA structures, such as R-loops, which can induce DNA breaks and genome instability. Paradoxically, as they relax DNA during transcription, topoisomerase enzymes introduce DNA breaks that can also endanger genome integrity. Stabilization of topoisomerases on chromatin by various anticancer drugs or by DNA alterations, can interfere with transcription machinery and cause permanent DNA breaks and R-loops. Here, we review the role of transcription in mediating DNA breaks, and discuss how deregulation of topoisomerase activity can impact on transcription and DNA break formation, and its connection with cancer.
Collapse
Affiliation(s)
- Agnese Cristini
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.
| | - Mathéa Géraud
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.
| |
Collapse
|
15
|
G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target. J Bacteriol 2021; 203:e0057720. [PMID: 33649149 DOI: 10.1128/jb.00577-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA strands consisting of multiple runs of guanines can adopt a noncanonical, four-stranded DNA secondary structure known as G-quadruplex or G4 DNA. G4 DNA is thought to play an important role in transcriptional and translational regulation of genes, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. In other organisms, including several bacterial pathogens and some plant species, the biological roles of G4 DNA and G4 RNA are starting to be explored. Recent investigations showed that G4 DNA and G4 RNA are generally conserved across plant species. In silico analyses of several bacterial genomes identified putative guanine-rich, G4 DNA-forming sequences in promoter regions. The sequences were particularly abundant in certain gene classes, suggesting that these highly diverse structures can be employed to regulate the expression of genes involved in secondary metabolite synthesis and signal transduction. Furthermore, in the pathogen Mycobacterium tuberculosis, the distribution of G4 motifs and their potential role in the regulation of gene transcription advocate for the use of G4 ligands to develop novel antitubercular therapies. In this review, we discuss the various roles of G4 structures in bacterial DNA and the application of G4 DNA as inhibitors or therapeutic agents to address bacterial pathogens.
Collapse
|
16
|
Miglietta G, Russo M, Capranico G. G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders. Nucleic Acids Res 2020; 48:11942-11957. [PMID: 33137181 PMCID: PMC7708042 DOI: 10.1093/nar/gkaa944] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.
Collapse
Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| |
Collapse
|
17
|
Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
Collapse
Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| |
Collapse
|
18
|
Kota S, Chaudhary R, Mishra S, Misra HS. Topoisomerase IB interacts with genome segregation proteins and is involved in multipartite genome maintenance in Deinococcus radiodurans. Microbiol Res 2020; 242:126609. [PMID: 33059113 DOI: 10.1016/j.micres.2020.126609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
Deinococcus radiodurans, an extremophile, resistant to many abiotic stresses including ionizing radiation, has 2 type I topoisomerases (drTopo IA and drTopo IB) and one type II topoisomerase (DNA gyrase). The role of drTopo IB in guanine quadruplex DNA (G4 DNA) metabolism was demonstrated earlier in vitro. Here, we report that D. radiodurans cells lacking drTopo IB (ΔtopoIB) show sensitivity to G4 DNA binding drug (NMM) under normal growth conditions. The activity of G4 motif containing promoters like mutL and recQ was reduced in the presence of NMM in mutant cells. In mutant, the percentage of anucleate cells was more while the copy number of genome elements were less as compared to wild type. Protein-protein interaction studies showed that drTopo IB interacts with genome segregation and DNA replication initiation (DnaA) proteins. The typical patterns of cellular localization of GFP-PprA were affected in the mutant cells. Microscopic examination of D. radiodurans cells expressing drTopo IB-RFP showed its localization on nucleoid forming a streak parallel to the old division septum and perpendicular to newly formed septum. These results together suggest the role of drTopo IB in genome maintenance in this bacterium.
Collapse
Affiliation(s)
- Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India.
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India.
| |
Collapse
|
19
|
Rauser V, Weinhold E. Quantitative Formation of Monomeric G-Quadruplex DNA from Multimeric Structures of c-Myc Promoter Sequence. Chembiochem 2020; 21:2445-2448. [PMID: 32267052 PMCID: PMC7496815 DOI: 10.1002/cbic.202000159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/07/2020] [Indexed: 12/02/2022]
Abstract
G‐Quadruplex (G4)‐forming DNA sequences have a tendency to form stable multimeric structures. This can be problematic for studies with synthetic oligodeoxynucleotides. Herein, we describe a method that quantitatively converts multimeric intermolecular structures of the Pu27 sequence from the c‐myc promoter into the desired monomeric G4 by alkaline treatment and refolding.
Collapse
Affiliation(s)
- Valerie Rauser
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| |
Collapse
|
20
|
Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
Collapse
Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
| |
Collapse
|
21
|
The Functional Consequences of Eukaryotic Topoisomerase 1 Interaction with G-Quadruplex DNA. Genes (Basel) 2020; 11:genes11020193. [PMID: 32059547 PMCID: PMC7073998 DOI: 10.3390/genes11020193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/22/2022] Open
Abstract
Topoisomerase I in eukaryotic cells is an important regulator of DNA topology. Its catalytic function is to remove positive or negative superhelical tension by binding to duplex DNA, creating a reversible single-strand break, and finally religating the broken strand. Proper maintenance of DNA topological homeostasis, in turn, is critically important in the regulation of replication, transcription, DNA repair, and other processes of DNA metabolism. One of the cellular processes regulated by the DNA topology and thus by Topoisomerase I is the formation of non-canonical DNA structures. Non-canonical or non-B DNA structures, including the four-stranded G-quadruplex or G4 DNA, are potentially pathological in that they interfere with replication or transcription, forming hotspots of genome instability. In this review, we first describe the role of Topoisomerase I in reducing the formation of non-canonical nucleic acid structures in the genome. We further discuss the interesting recent discovery that Top1 and Top1 mutants bind to G4 DNA structures in vivo and in vitro and speculate on the possible consequences of these interactions.
Collapse
|
22
|
Kim N. The Interplay between G-quadruplex and Transcription. Curr Med Chem 2019; 26:2898-2917. [PMID: 29284393 PMCID: PMC6026074 DOI: 10.2174/0929867325666171229132619] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
G4 DNA is a non-canonical DNA structure consisting of a stacked array of Gquartets held together by base pairing between guanine bases. The formation of G4 DNA requires a cluster of guanine-runs within a strand of DNA. Even though the chemistry of this remarkable DNA structure has been under investigation for decades, evidence supporting the biological relevance of G4 DNA has only begun to emerge and point to very important and conserved biological functions. This review will specifically focus on the interplay between transcription and G4 DNA and discuss two alternative but interconnected perspectives. The first part of the review will describe the evidence substantiating the intriguing idea that a shift in DNA structural conformation could be another layer of non-genetic or epigenetic regulator of gene expression and thereby an important determinant of cell fate. The second part will describe the recent genetic studies showing that those genomic loci containing G4 DNA-forming guanine-rich sequences are potential hotspots of genome instability and that the level and orientation of transcription is critical in the materialization of genome instability associated with these sequences.
Collapse
Affiliation(s)
- Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston; The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
| |
Collapse
|
23
|
Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid⁻Protein Interaction. Molecules 2019; 24:molecules24030396. [PMID: 30678288 PMCID: PMC6384609 DOI: 10.3390/molecules24030396] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
G-quadruplex is a special secondary structure of nucleic acids in guanine-rich sequences of genome. G-quadruplexes have been proved to be involved in the regulation of replication, DNA damage repair, and transcription and translation of oncogenes or other cancer-related genes. Therefore, targeting G-quadruplexes has become a novel promising anti-tumor strategy. Different kinds of small molecules targeting the G-quadruplexes have been designed, synthesized, and identified as potential anti-tumor agents, including molecules directly bind to the G-quadruplex and molecules interfering with the binding between the G-quadruplex structures and related binding proteins. This review will explore the feasibility of G-quadruplex ligands acting as anti-tumor drugs, from basis to application. Meanwhile, since helicase is the most well-defined G-quadruplex-related protein, the most extensive research on the relationship between helicase and G-quadruplexes, and its meaning in drug design, is emphasized.
Collapse
|
24
|
Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
Collapse
Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
| |
Collapse
|
25
|
Abstract
Topoisomerase I (Top1) resolves torsional stress that accumulates during transcription, replication and chromatin remodeling by introducing a transient single-strand break in DNA. The cleavage activity of Top1 has opposing roles, either promoting or destabilizing genome integrity depending on the context. Resolution of transcription-associated negative supercoils, for example, prevents pairing of the nascent RNA with the DNA template (R-loops) as well as DNA secondary structure formation. Reduced Top1 levels thus enhance CAG repeat contraction, somatic hypermutation, and class switch recombination. Actively transcribed ribosomal DNA is also destabilized in the absence of Top1, reflecting the importance of Top1 in ensuring efficient transcription. In terms of promoting genome instability, an aborted Top1 catalytic cycle stimulates deletions at short tandem repeats and the enzyme's transesterification activity supports illegitimate recombination. Finally, Top1 incision at ribonucleotides embedded in DNA generates deletions in tandem repeats, and induces gross chromosomal rearrangements and mitotic recombination.
Collapse
Affiliation(s)
- Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, CARL 384, Durham, NC, 27710, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, CARL 384, Durham, NC, 27710, USA.
| |
Collapse
|
26
|
Multi-targeted effects of G4-aptamers and their antiproliferative activity against cancer cells. Biochimie 2017; 145:163-173. [PMID: 29208488 DOI: 10.1016/j.biochi.2017.11.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022]
Abstract
We selected and investigated nine G-quadruplex (G4)-forming aptamers originally designed against different proteins involved in the regulation of cellular proliferation (STAT3, nucleolin, TOP1, SP1, VEGF, and SHP-2) and considered to be potential anticancer agents. We showed that under physiological conditions all the aptamers form stable G4s of different topology. G4 aptamers designed against STAT3, nucleolin and SP1 inhibit STAT3 transcriptional activity in human breast adenocarcinoma MCF-7 cells, and all the studied aptamers inhibit TOP1-mediated relaxation of supercoiled plasmid DNA. STAT3 inhibition by G4 aptamer designed against SP1 protein provides a new explanation for the SP1 and STAT3 crosstalk described recently. We found some correlation between G4-mediated inhibition of the DNA replication and TOP1 activity. Four G4 aptamers from our dataset that appeared to be the strongest TOP1 inhibitors most efficiently decreased de novo DNA synthesis, by up to 79-87%. Seven G4 aptamers demonstrated significantly higher antiproliferative activity on human breast adenocarcinoma MCF-7 cells than on immortalized mammary epithelial MCF-10A cells. Pleiotropic properties of G4 aptamers and their high specificity against cancer cells observed for the majority of the studied G4 aptamers allowed us to present them as promising candidates for multi-targeted cancer therapy.
Collapse
|
27
|
Lopez CR, Singh S, Hambarde S, Griffin WC, Gao J, Chib S, Yu Y, Ira G, Raney KD, Kim N. Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA. Nucleic Acids Res 2017; 45:5850-5862. [PMID: 28369605 PMCID: PMC5449603 DOI: 10.1093/nar/gkx201] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/15/2017] [Indexed: 01/05/2023] Open
Abstract
G-quadruplex or G4 DNA is a non-B secondary DNA structure consisting of a stacked array of guanine-quartets that can disrupt critical cellular functions such as replication and transcription. When sequences that can adopt Non-B structures including G4 DNA are located within actively transcribed genes, the reshaping of DNA topology necessary for transcription process stimulates secondary structure-formation thereby amplifying the potential for genome instability. Using a reporter assay designed to study G4-induced recombination in the context of an actively transcribed locus in Saccharomyces cerevisiae, we tested whether co-transcriptional activator Sub1, recently identified as a G4-binding factor, contributes to genome maintenance at G4-forming sequences. Our data indicate that, upon Sub1-disruption, genome instability linked to co-transcriptionally formed G4 DNA in Top1-deficient cells is significantly augmented and that its highly conserved DNA binding domain or the human homolog PC4 is sufficient to suppress G4-associated genome instability. We also show that Sub1 interacts specifically with co-transcriptionally formed G4 DNA in vivo and that yeast cells become highly sensitivity to G4-stabilizing chemical ligands by the loss of Sub1. Finally, we demonstrate the physical and genetic interaction of Sub1 with the G4-resolving helicase Pif1, suggesting a possible mechanism by which Sub1 suppresses instability at G4 DNA.
Collapse
Affiliation(s)
- Christopher R Lopez
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Shivani Singh
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Shashank Hambarde
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wezley C Griffin
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Shubeena Chib
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Yang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| |
Collapse
|
28
|
Abstract
Topoisomerases manage the torsional stress associated with the separation of DNA strands during transcription and DNA replication. Eukaryotic Topoisomerase I (Top1) is a Type IB enzyme that nicks and rejoins only one strand of duplex DNA, and it is especially important during transcription. By resolving transcription-associated torsional stress, Top1 reduces the accumulation of genome-destabilizing R-loops and non-B DNA structures. The DNA nicking activity of Top1, however, can also initiate genome instability in the form of illegitimate recombination, homologous recombination and mutagenesis. In this review, we focus on the diverse, and often opposing, roles of Top1 in regulating eukaryotic genome stability.
Collapse
|
29
|
Rigo R, Palumbo M, Sissi C. G-quadruplexes in human promoters: A challenge for therapeutic applications. Biochim Biophys Acta Gen Subj 2016; 1861:1399-1413. [PMID: 28025083 DOI: 10.1016/j.bbagen.2016.12.024] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND G-rich sequences undergo unique structural equilibria to form G-quadruplexes (G4) both in vitro and in cell systems. Several pathologies emerged to be directly related to G4 occurrence at defined genomic portions. Additionally, G-rich sequences are significantly represented around transcription start sites (TSS) thus leading to the hypothesis of a gene regulatory function for G4. Thus, the tuning of G4 formation has been proposed as a new powerful tool to regulate gene expression to treat related pathologies. However, up-to date this approach did not provide any new really efficient treatment. SCOPE OF REVIEW Here, we summarize the most recent advances on the correlation between the structural features of G4 in human promoters and the role these systems physiologically exert. In particular we focus on the effect of G4 localization among cell compartments and along the promoters in correlation with protein interaction networks and epigenetic state. Finally the intrinsic structural features of G4 at promoters are discussed to unveil the contribution of different G4 structural modules in this complex architecture. MAJOR CONCLUSIONS It emerges that G4s play several roles in the intriguing and complex mechanism of gene expression, being able to produce opposite effects on the same target. This reflects the occurrence of a highly variegate network of several components working simultaneously. GENERAL SIGNIFICANCE The resulting picture is still fuzzy but some points of strength are definitely emerging, which prompts all of us to strengthen our efforts in view of a selective control of gene expression through G4 modulation. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Riccardo Rigo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo, 5, 35131 Padova, Italy
| | - Manlio Palumbo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo, 5, 35131 Padova, Italy
| | - Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo, 5, 35131 Padova, Italy.
| |
Collapse
|
30
|
Cammas A, Dubrac A, Morel B, Lamaa A, Touriol C, Teulade-Fichou MP, Prats H, Millevoi S. Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation. RNA Biol 2015; 12:320-9. [PMID: 25826664 DOI: 10.1080/15476286.2015.1017236] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The activation of translation contributes to malignant transformation and is an emerging target for cancer therapies. RNA G-quadruplex structures are general inhibitors of cap-dependent mRNA translation and were recently shown to be targeted for oncoprotein translational activation. In contrast however, the G-quadruplex within the 5'UTR of the human vascular endothelial growth factor A (VEGF) has been shown to be essential for IRES-mediated translation. Since VEGF has a pivotal role in tumor angiogenesis and is a major target of anti-tumoral therapies, we investigated the structure/function relationship of the VEGF G-quadruplex and defined whether it could have a therapeutic potential. We found that the G-quadruplex within the VEGF IRES is dispensable for cap-independent function and activation in stress conditions. However, stabilization of the VEGF G-quadruplex by increasing the G-stretches length or by replacing it with the one of NRAS results in strong inhibition of IRES-mediated translation of VEGF. We also demonstrate that G-quadruplex ligands stabilize the VEGF G-quadruplex and inhibit cap-independent translation in vitro. Importantly, the amount of human VEGF mRNA associated with polysomes decreases in the presence of a highly selective stabilizing G-quadruplex ligand, resulting in reduced VEGF protein expression. Together, our results uncover the existence of functionally silent G-quadruplex structures that are susceptible to conversion into efficient repressors of cap-independent mRNA translation. These findings have implications for the in vivo applications of G-quadruplex-targeting compounds and for anti-angiogenic therapies.
Collapse
Affiliation(s)
- Anne Cammas
- a Inserm UMR 1037- University of Toulouse III; Cancer Research Center of Toulouse (CRCT) ; Toulouse, France
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Topoisomerase IB of Deinococcus radiodurans resolves guanine quadruplex DNA structures in vitro. J Biosci 2015; 40:833-43. [DOI: 10.1007/s12038-015-9571-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
32
|
Yadav P, Owiti N, Kim N. The role of topoisomerase I in suppressing genome instability associated with a highly transcribed guanine-rich sequence is not restricted to preventing RNA:DNA hybrid accumulation. Nucleic Acids Res 2015; 44:718-29. [PMID: 26527723 PMCID: PMC4737143 DOI: 10.1093/nar/gkv1152] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Highly transcribed guanine-run containing sequences, in Saccharomyces cerevisiae, become unstable when topoisomerase I (Top1) is disrupted. Topological changes, such as the formation of extended RNA:DNA hybrids or R-loops or non-canonical DNA structures including G-quadruplexes has been proposed as the major underlying cause of the transcription-linked genome instability. Here, we report that R-loop accumulation at a guanine-rich sequence, which is capable of assembling into the four-stranded G4 DNA structure, is dependent on the level and the orientation of transcription. In the absence of Top1 or RNase Hs, R-loops accumulated to substantially higher extent when guanine-runs were located on the non-transcribed strand. This coincides with the orientation where higher genome instability was observed. However, we further report that there are significant differences between the disruption of RNase Hs and Top1 in regards to the orientation-specific elevation in genome instability at the guanine-rich sequence. Additionally, genome instability in Top1-deficient yeasts is not completely suppressed by removal of negative supercoils and further aggravated by expression of mutant Top1. Together, our data provide a strong support for a function of Top1 in suppressing genome instability at the guanine-run containing sequence that goes beyond preventing the transcription-associated RNA:DNA hybrid formation.
Collapse
Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Norah Owiti
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| |
Collapse
|
33
|
Ogloblina AM, Bannikova VA, Khristich AN, Oretskaya TS, Yakubovskaya MG, Dolinnaya NG. Parallel G-quadruplexes formed by guanine-rich microsatellite repeats inhibit human topoisomerase I. BIOCHEMISTRY (MOSCOW) 2015; 80:1026-38. [DOI: 10.1134/s0006297915080088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
34
|
Smaldino PJ, Routh ED, Kim JH, Giri B, Creacy SD, Hantgan RR, Akman SA, Vaughn JP. Mutational Dissection of Telomeric DNA Binding Requirements of G4 Resolvase 1 Shows that G4-Structure and Certain 3'-Tail Sequences Are Sufficient for Tight and Complete Binding. PLoS One 2015; 10:e0132668. [PMID: 26172836 PMCID: PMC4501837 DOI: 10.1371/journal.pone.0132668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 06/18/2015] [Indexed: 11/18/2022] Open
Abstract
Ends of human chromosomes consist of the six nucleotide repeat d[pTTAGGG]n known as telomeric DNA, which protects chromosomes. We have previously shown that the DHX36 gene product, G4 Resolvase 1 (G4R1), binds parallel G-quadruplex (G4) DNA with an unusually tight apparent Kd. Recent work associates G4R1 with the telomerase holoenzyme, which may allow it to access telomeric G4-DNA. Here we show that G4R1 can tightly bind telomeric G4-DNA, and in the context of the telomeric sequence, we determine length, sequence, and structural requirements sufficient for tight G4R1 telomeric binding. Specifically, G4R1 binds telomeric DNA in the K+-induced "3+1" G4-topology with an apparent Kd = 10 ± 1.9 pM, a value similar as previously found for binding to unimolecular parallel G4-DNA. G4R1 binds to the Na+-induced "2+2" basket G4-structure formed by the same DNA sequence with an apparent Kd = 71 ± 2.2 pM. While the minimal G4-structure is not sufficient for G4R1 binding, a 5' G4-structure with a 3' unstructured tail containing a guanine flanked by adenine(s) is sufficient for maximal binding. Mutations directed to disrupt G4-structure similarly disrupt G4R1 binding; secondary mutations that restore G4-structure also restore G4R1 binding. We present a model showing that a replication fork disrupting a T-loop could create a 5' quadruplex with an opened 3'tail structure that is recognized by G4R1.
Collapse
Affiliation(s)
- Philip J. Smaldino
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, United States of America
| | - Eric D. Routh
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, United States of America
| | - Jung H. Kim
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, United States of America
| | - Banabihari Giri
- Department of Chemistry, Furman University, Greenville, South Carolina, 29613, United States of America
| | - Steven D. Creacy
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, United States of America
- Harmonyx Diagnostics, Cordova, Tennessee, 38016, United States of America
| | - Roy R. Hantgan
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, United States of America
| | - Steven A. Akman
- Department of Hematology and Oncology, Roper St. Francis Hospital, Charleston, South Carolina, 29401, United States of America
| | - James P. Vaughn
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157, United States of America
- * E-mail:
| |
Collapse
|
35
|
Parrino B, Carbone A, Ciancimino C, Spanò V, Montalbano A, Barraja P, Cirrincione G, Diana P, Sissi C, Palumbo M, Pinato O, Pennati M, Beretta G, Folini M, Matyus P, Balogh B, Zaffaroni N. Water-soluble isoindolo[2,1-a]quinoxalin-6-imines: in vitro antiproliferative activity and molecular mechanism(s) of action. Eur J Med Chem 2015; 94:149-62. [PMID: 25768699 DOI: 10.1016/j.ejmech.2015.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/29/2015] [Accepted: 03/03/2015] [Indexed: 12/31/2022]
Abstract
Water-soluble isoindoloquinoxalin (IIQ) imines and the corresponding acetates were conveniently prepared from the key intermediates 2-(2'-aminophenyl)-2H-isoindole-1-carbonitriles obtained by a Strecker reaction between substituted 1,2-dicarbaldehydes and 1,2-phenylenediamines. Both series were screened by the National Cancer Institute (Bethesda, MD) and showed potent antiproliferative activity against a panel of 60 human tumor cell lines. Several of the novel compounds showed GI50 values at a nanomolar level on the majority of the tested cell lines. Among IIQ derivatives, methoxy substituents at positions 3 and 8 or/and 9 were especially effective in impairing cell cycle progression and inducing apoptosis in cancer cells. These effects were associated to IIQ-mediated impairment of tubulin polymerization at pharmacologically significant concentrations of tested compounds. In addition, impaired DNA topoisomerase I functions and perturbation in telomere architecture were observed in cells exposed to micromolar concentrations of IIQ derivatives. The above results suggest that IIQ derivatives exhibit multi-target cytotoxic activities.
Collapse
Affiliation(s)
- Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Carbone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Cristina Ciancimino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Virginia Spanò
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy.
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, Via Marzolo 5, 35131 Padova, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, Via Marzolo 5, 35131 Padova, Italy
| | - Odra Pinato
- Department of Pharmaceutical and Pharmacological Sciences, Via Marzolo 5, 35131 Padova, Italy
| | - Marzia Pennati
- Dept. of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Via Amadeo 42, Milano, Italy
| | - Giovanni Beretta
- Dept. of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Via Amadeo 42, Milano, Italy
| | - Marco Folini
- Dept. of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Via Amadeo 42, Milano, Italy
| | - Peter Matyus
- Department of Organic Chemistry, Semmelweis University, Högyes E. u. 7, H-1092 Budapest, Hungary
| | - Balázs Balogh
- Department of Organic Chemistry, Semmelweis University, Högyes E. u. 7, H-1092 Budapest, Hungary
| | - Nadia Zaffaroni
- Dept. of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Via Amadeo 42, Milano, Italy
| |
Collapse
|
36
|
Yadav P, Harcy V, Argueso JL, Dominska M, Jinks-Robertson S, Kim N. Topoisomerase I plays a critical role in suppressing genome instability at a highly transcribed G-quadruplex-forming sequence. PLoS Genet 2014; 10:e1004839. [PMID: 25473964 PMCID: PMC4256205 DOI: 10.1371/journal.pgen.1004839] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
G-quadruplex or G4 DNA is a non-B secondary DNA structure that comprises a stacked array of guanine-quartets. Cellular processes such as transcription and replication can be hindered by unresolved DNA secondary structures potentially endangering genome maintenance. As G4-forming sequences are highly frequent throughout eukaryotic genomes, it is important to define what factors contribute to a G4 motif becoming a hotspot of genome instability. Using a genetic assay in Saccharomyces cerevisiae, we previously demonstrated that a potential G4-forming sequence derived from a guanine-run containing immunoglobulin switch Mu (Sμ) region becomes highly unstable when actively transcribed. Here we describe assays designed to survey spontaneous genome rearrangements initiated at the Sμ sequence in the context of large genomic areas. We demonstrate that, in the absence of Top1, a G4 DNA-forming sequence becomes a strong hotspot of gross chromosomal rearrangements and loss of heterozygosity associated with mitotic recombination within the ∼20 kb or ∼100 kb regions of yeast chromosome V or III, respectively. Transcription confers a critical strand bias since genome rearrangements at the G4-forming Sμ are elevated only when the guanine-runs are located on the non-transcribed strand. The direction of replication and transcription, when in a head-on orientation, further contribute to the elevated genome instability at a potential G4 DNA-forming sequence. The implications of our identification of Top1 as a critical factor in suppression of instability associated with potential G4 DNA-forming sequences are discussed. Genome instability is not evenly distributed, but rather is highly elevated at certain genomic loci containing DNA sequences that can fold into non-canonical secondary structures. The four-stranded G-quadruplex or G4 DNA is one such DNA structure capable of instigating transcription and/or replication obstruction and subsequent genome instability. In this study, we used a reporter system to quantitatively measure the level of genome instability occurring at a G4 DNA motif integrated into the yeast genome. We showed that the disruption of Topoisomerase I function significantly elevated various types of genome instability at the highly transcribed G4 motif generating loss of heterozygosity and copy number alterations (deletions and duplications), both of which are frequently observed in cancer genomes.
Collapse
Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Victoria Harcy
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
37
|
DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
Collapse
|
38
|
Bharti SK, Sommers JA, Zhou J, Kaplan DL, Spelbrink JN, Mergny JL, Brosh RM. DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative Twinkle helicase. J Biol Chem 2014; 289:29975-93. [PMID: 25193669 DOI: 10.1074/jbc.m114.567073] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mitochondrial replication are not well understood. In this work, we performed a computational analysis of the human mitochondrial genome using the "Pattern Finder" G-quadruplex (G4) predictor algorithm to assess whether G4-forming sequences reside in close proximity (within 20 base pairs) to known mitochondrial DNA deletion breakpoints. We then used this information to map G4P sequences with deletions characteristic of representative mitochondrial genetic disorders and also those identified in various cancers and aging. Circular dichroism and UV spectral analysis demonstrated that mitochondrial G-rich sequences near deletion breakpoints prevalent in human disease form G-quadruplex DNA structures. A biochemical analysis of purified recombinant human Twinkle protein (gene product of c10orf2) showed that the mitochondrial replicative helicase inefficiently unwinds well characterized intermolecular and intramolecular G-quadruplex DNA substrates, as well as a unimolecular G4 substrate derived from a mitochondrial sequence that nests a deletion breakpoint described in human renal cell carcinoma. Although G4 has been implicated in the initiation of mitochondrial DNA replication, our current findings suggest that mitochondrial G-quadruplexes are also likely to be a source of instability for the mitochondrial genome by perturbing the normal progression of the mitochondrial replication machinery, including DNA unwinding by Twinkle helicase.
Collapse
Affiliation(s)
- Sanjay Kumar Bharti
- From the Laboratory of Molecular Gerontology, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224
| | - Joshua A Sommers
- From the Laboratory of Molecular Gerontology, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224
| | - Jun Zhou
- the ARNA Laboratory, University of Bordeaux, F-33000 Bordeaux, France, INSERM U869, Institut Européen de Chimie et Biologie (IECB), F-33600 Pessac, France
| | - Daniel L Kaplan
- the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32312
| | - Johannes N Spelbrink
- the FinMIT Centre of Excellence, BioMediTech and Tampere University Hospital, Pirkanmaa Hospital District, University of Tampere, FI-33014 Tampere, Finland, and the Department of Pediatrics, Nijmegan Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P. O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jean-Louis Mergny
- the ARNA Laboratory, University of Bordeaux, F-33000 Bordeaux, France, INSERM U869, Institut Européen de Chimie et Biologie (IECB), F-33600 Pessac, France
| | - Robert M Brosh
- From the Laboratory of Molecular Gerontology, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224,
| |
Collapse
|
39
|
Lai H, Xiao Y, Yan S, Tian F, Zhong C, Liu Y, Weng X, Zhou X. Symmetric cyanovinyl-pyridinium triphenylamine: a novel fluorescent switch-on probe for an antiparallel G-quadruplex. Analyst 2014; 139:1834-8. [DOI: 10.1039/c3an02269b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe a probe based on a cyanovinyl pyridinium triphenylamine (CPT) derivative, which showed fluorescent switch-on properties toward an antiparallel G-quadruplex.
Collapse
Affiliation(s)
- Hai Lai
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Yijie Xiao
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Shengyong Yan
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Fangfang Tian
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Cheng Zhong
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Yi Liu
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
- The State Key Laboratory of Natural and Biomimetic Drugs
- State
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
- The State Key Laboratory of Natural and Biomimetic Drugs
- State
| |
Collapse
|
40
|
Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Gorelick RJ, Sugiyama H. HIV-1 nucleocapsid proteins as molecular chaperones for tetramolecular antiparallel G-quadruplex formation. J Am Chem Soc 2013; 135:18575-85. [PMID: 24224650 PMCID: PMC3898174 DOI: 10.1021/ja409085j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.
Collapse
Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Phong Lan Thao Tran
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Robert J. Gorelick
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, P. O. Box B, Frederick, Maryland 21702-1201, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| |
Collapse
|
41
|
Zhou J, Abramov M, Liu F, Amrane S, Bourdoncle A, Herdewijn P, Mergny JL. Effects of six-membered carbohydrate rings on structure, stability, and kinetics of G-quadruplexes. Chemistry 2013; 19:14719-25. [PMID: 24027098 DOI: 10.1002/chem.201301743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/24/2013] [Indexed: 12/13/2022]
Abstract
We have evaluated the conformational, thermal, and kinetic properties of d(TGGGGT) analogues with one or five of the ribose nucleotides replaced with the carbohydrate residues hexitol nucleic acid (HNA), cyclohexenyl nucleic acid (CeNA), or altritol nucleic acid (ANA). All of the modified oligonucleotides formed G-quadruplexes, but substitution with the six-membered rings resulted in a mixture of G-quadruplex structures. UV and CD melting analyses showed that the structure formed by d(TGGGGT) modified with HNA was stabilized whereas that modified with CeNA was destabilized, relative to the structure formed by the unmodified oligonucleotide. Substitution at the fourth base of the G-tract with ANA resulted in a greater stabilization effect than substitution at the first G residue; substitution with five ANA residues resulted in significant stabilization of the G-quadruplex. A single substitution with CeNA at the first base of the G-tract or five substitutions with HNA resulted in striking deceleration or acceleration of G-quadruplex formation, respectively. Our results shed light on the effect of the sugar moiety on the properties of G-quadruplex structures.
Collapse
Affiliation(s)
- Jun Zhou
- Univ. Bordeaux, ARNA Laboratory, 33000 Bordeaux (France); INSERM, U869, IECB, 33600 Pessac (France), Fax: (+33) 5-4000-3004
| | | | | | | | | | | | | |
Collapse
|
42
|
Samatanga B, Dominguez C, Jelesarov I, Allain FHT. The high kinetic stability of a G-quadruplex limits hnRNP F qRRM3 binding to G-tract RNA. Nucleic Acids Res 2012; 41:2505-16. [PMID: 23275549 PMCID: PMC3575826 DOI: 10.1093/nar/gks1289] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The RNA binding protein heterogeneous nuclear ribonucleoprotein (hnRNP) F is involved in telomeres maintenance and pre-mRNA processing, such as alternative splicing and polyadenylation. It specifically recognizes RNA containing three consecutive guanines (G-tracts) that have the potential to assemble into G-quadruplexes. We have proposed recently that hnRNP F could regulate alternative splicing by remodeling RNA structures, such as G-quadruplexes. However, the exact mechanism of hnRNP F binding to such RNA sequences remains unknown. Here, we have studied the binding of the third RNA binding domain of hnRNP F [quasi-RNA recognition motif 3 (qRRM3)] to G-tract RNA using isothermal titration calorimetry, circular dichroism and nuclear magnetic resonance spectroscopy. Our results show that qRRM3 binds specifically exclusively to single-stranded G-tracts (ssRNA), in contrast to previous reports stating that the G-quadruplex was recognized as well. Furthermore, we demonstrate that the pre-existent ssRNA/G-quadruplex equilibrium slows down the formation of the protein–ssRNA complex. Based on in vitro transcription assays, we show that the rate of the protein–RNA complex formation is faster than that of the G-quadruplex. We propose a model according to which hnRNP F could bind RNA co-transcriptionally and prevents G-quadruplex formation.
Collapse
Affiliation(s)
- Brighton Samatanga
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | | | | |
Collapse
|
43
|
Wang SR, Zhang D, Luo FL, Liu L, Weng XC, Huang J, Li GR, Zhang XL, Zhou X. Some cationic porphyrins: synthesis, stabilization of G-quadruplexes, and down-regulation of c-myc in Hep G2 cells. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609001121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The stabilization of G-quadruplex DNA represents an attractive strategy for the design and development of novel antitumor drugs. In the present work, we have designed and synthesized nine cationic porphyrins, each with four side arms at their meso positions. The interactions of these porphyrins with both human telomeric DNA and NHE III1 G-quadruplexes were measured by various DNA binding assays, including polymerase stop assay, circular dichroism (CD) and CD melting assay. We then proceeded to investigate their effects on the expression of c-myc oncogene in the Hep G2 cell line. The experimental results indicate that these porphyrins are capable of effectively inducing or stabilizing both human telomeric and NHE III1 G-quadruplexes in the presence or absence of metal ions. Furthermore, we have discovered that porphyrins with a stronger stabilizing effect on c-myc G-quadruplexes lead to more pronounced down-regulation of the c-myc oncogene in the Hep G2 cell line.
Collapse
Affiliation(s)
- Shao R. Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Dan Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Feng L. Luo
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Lin Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao C. Weng
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Jing Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Guo R. Li
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao L. Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| |
Collapse
|
44
|
|
45
|
Von ST, Seng HL, Lee HB, Ng SW, Kitamura Y, Chikira M, Ng CH. DNA molecular recognition and cellular selectivity of anticancer metal(II) complexes of ethylenediaminediacetate and phenanthroline: multiple targets. J Biol Inorg Chem 2011; 17:57-69. [DOI: 10.1007/s00775-011-0829-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 07/16/2011] [Indexed: 01/29/2023]
|
46
|
Sun H, Xiang J, Liu Y, Li L, Li Q, Xu G, Tang Y. A stabilizing and denaturing dual-effect for natural polyamines interacting with G-quadruplexes depending on concentration. Biochimie 2011; 93:1351-6. [DOI: 10.1016/j.biochi.2011.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 06/07/2011] [Indexed: 01/31/2023]
|
47
|
Abstract
DNA G-quadruplexes are DNA secondary structures formed in specific G-rich sequences. DNA sequences that can form G-quadruplexes have been found in regions with biological significance, such as human telomeres and oncogene-promoter regions. DNA G-quadruplexes have recently emerged as a new class of novel molecular targets for anticancer drugs. Recent progress on structural studies of the biologically relevant G-quadruplexes formed in human telomeres and in the promoter regions of human oncogenes will be discussed, as well as recent advances in the design and development of G-quadruplex-interactive drugs. DNA G-quadruplexes can readily form in solution under physiological conditions and are globularly folded nucleic acid structures. The molecular structures of intramolecular G-quadruplexes appear to differ from one another and, therefore, in principle may be differentially regulated and targeted by different proteins and drugs.
Collapse
|
48
|
Shuai L, Deng M, Zhang D, Zhou Y, Zhou X. Quadruplex-duplex motifs as new topoisomerase I inhibitors. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 29:841-53. [PMID: 21128171 DOI: 10.1080/15257770.2010.530635] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this article, 13 short chains that can form G-quadruplex and quadruplex-duplex motif have been designed. Fourteen oligonucleotides, including 13 short chains as well as a reference short chain all have certain level of inhibition to topoisomerase I, whether or not they form G-quadruplex and quadruplex-duplex motif, and the G-quadruplex and quadruplex-duplex motif show better activity than single short chain. The result confirmed that after forming G-quadruplex and quadruplex-duplex motif these 14 oligonucleotides are competitive inhibition, that is, through the priority binding with the topoisomerase I and precluding from its binding with the normal substrate pBR322 and, therefore, inhibiting the next reaction.
Collapse
Affiliation(s)
- Li Shuai
- College of Pharmacy, South-Central University for Nationalities, Hubei, Wuhan, P. R. China.
| | | | | | | | | |
Collapse
|
49
|
Biroccio A, Porru M, Rizzo A, Salvati E, D'Angelo C, Orlandi A, Passeri D, Franceschin M, Stevens MFG, Gilson E, Beretta G, Zupi G, Pisano C, Zunino F, Leonetti C. DNA damage persistence as determinant of tumor sensitivity to the combination of Topo I inhibitors and telomere-targeting agents. Clin Cancer Res 2011; 17:2227-36. [PMID: 21355072 DOI: 10.1158/1078-0432.ccr-10-3033] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE We previously reported that the G-quadruplex (G4) ligand RHPS4 potentiates the antitumor activity of camptothecins both in vitro and in tumor xenografts. The present study aims at investigating the mechanisms involved in this specific drug interaction. EXPERIMENTAL DESIGN Combination index test was used to evaluate the interaction between G4 ligands and standard or novel Topo I inhibitors. Chromatin immunoprecipitation was performed to study the presence at telomeres of various types of topisomerase, while immunolabeling experiments were performed to measure the activation of DNA damage both in vitro and in tumor xenografts. RESULTS We report that integration of the Topo I inhibitor SN-38, but not the Topo II poison doxorubicin with telomere-based therapy is strongly effective and the sequence of drug administration is critical in determining the synergistic interaction, impairing the cell ability to recover from drug-induced cytotoxicity. The synergistic effect of this combination was also observed by using novel camptothecins and, more interestingly, mice treated with ST1481/RHPS4 combination showed an inhibition and delay of tumor growth as well as an increased survival. The study of the mechanism(s) revealed that treatment with G4 ligands increased Topo I at the telomeres and the functional relevance of this observation was directly assessed by showing that standard and novel camptothecins stabilized DNA damage both in vitro and in xenografts. CONCLUSIONS Our results demonstrate an outstanding efficacy of Topo I inhibitors/G4 ligands combination, which likely reflects an enhanced and persistent activation of DNA damage response as a critical determinant of the therapeutic improvement.
Collapse
Affiliation(s)
- Annamaria Biroccio
- Experimental Chemotherapy Laboratory, Regina Elena Cancer Institute, Tor Vergata University, Rome, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Zhou W, Brand NJ, Ying L. G-quadruplexes-novel mediators of gene function. J Cardiovasc Transl Res 2011; 4:256-70. [PMID: 21302011 DOI: 10.1007/s12265-011-9258-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 01/24/2011] [Indexed: 11/30/2022]
Abstract
Since the famous double-helix model was proposed, chromosomal DNA has been regarded as a rigid molecule containing the genetic information of an organism. It is clear now that DNA can adopt many transient, complex structures that can perform different biological functions. The G4 DNA (also called DNA G-quadruplex or G-tetraplex), a four-stranded DNA structure composed of stacked G-tetrads (guanine tetrads), has attracted much attention during the past two decades due to its ability to adopt a variety of structures and its possible biological functions. This review gives a glimpse on the structural diversity and biophysical properties of these fascinating DNA structures. Common methods that are widely used in investigating biophysical properties and biological functions of G4 DNA are described briefly. Next, bioinformatics studies that indicate evidence of evolutionary selection and potential functions of G4 DNA are discussed. Finally, examples of various biological functions of different G4 DNA are given, and potential roles of G4 DNA in respect of cardiovascular science are discussed.
Collapse
Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, UK.
| | | | | |
Collapse
|