1
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Mugunthan S, Wong LL, Winnerdy FR, Summers S, Bin Ismail MH, Foo YH, Jaggi TK, Meldrum OW, Tiew PY, Chotirmall SH, Rice SA, Phan AT, Kjelleberg S, Seviour T. RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms. Nat Commun 2023; 14:7772. [PMID: 38012164 PMCID: PMC10682433 DOI: 10.1038/s41467-023-43533-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
The extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.
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Affiliation(s)
- Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- St John's Island National Marine Laboratory c/o Tropical Marine Science Institute, National University of Singapore, 119227, Singapore
| | | | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), Nanyang Technological University, Singapore, 636921, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Oliver W Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- The iThree Institute, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Canberra, Australia
| | - Anh Tuân Phan
- School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, 8000, Denmark.
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2
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Papp C, Jenjaroenpun P, Mukundan VT, Phan AT, Kuznetsov VA. Dataset of bulged G-quadruplex forming sequences in the human genome. Data Brief 2023; 50:109550. [PMID: 37743888 PMCID: PMC10515301 DOI: 10.1016/j.dib.2023.109550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
When several continuous guanine runs are present closely in a nucleic acid sequence, a secondary structure called G-quadruplex can form (G4s). Such structures in the genome could serve as structural and functional regulators in gene expression, DNA-protein binding, epigenetic modification, and genotoxic stress. Several types of G4-forming DNA sequences exist, including bulged G4-forming sequences (G4-BS). Such bulges occur due to the presence of non-guanine bases in specific locations (G-runs) in the G4-forming sequences. At present, search algorithms do not identify stable G4-BS conformations, making genome-wide studies of G4-like structures difficult. Data provided in this study are related to a published article "Stable bulged G-quadruplexes in the human genome: Identification, experimental validation and functionalization" published by Nucleic Acids Research [DIO.org/10.193/nar/gkad252]. Based on our studies in vitro and G4-seq and G4 CUT&Tag data analysis, we have specified and validated three pG4-BS models. In this article, a large collection of 'raw' (unfiltered) dataset is presented, which includes three subfamilies of pG4-BS. For each of pG4-BS, we provide strand-specific genomic boundaries. Data on pG4-BS might be useful in elucidating their structural, functional, and evolutionary roles. Furthermore, they may provide insight into the pathobiology of G4-like structures and their potential therapeutic applications.
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Affiliation(s)
- Csaba Papp
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Vineeth T. Mukundan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Vladimir A. Kuznetsov
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
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3
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Korsakova A, Phan AT. Prediction of G4 formation in live cells with epigenetic data: a deep learning approach. NAR Genom Bioinform 2023; 5:lqad071. [PMID: 37636021 PMCID: PMC10448861 DOI: 10.1093/nargab/lqad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/25/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
G-quadruplexes (G4s) are secondary structures abundant in DNA that may play regulatory roles in cells. Despite the ubiquity of the putative G-quadruplex-forming sequences (PQS) in the human genome, only a small fraction forms G4 structures in cells. Folded G4, histone methylation and chromatin accessibility are all parts of the complex cis regulatory landscape. We propose an approach for prediction of G4 formation in cells that incorporates epigenetic and chromatin accessibility data. The novel approach termed epiG4NN efficiently predicts cell-specific G4 formation in live cells based on a local epigenomic snapshot. Our results confirm the close relationship between H3K4me3 histone methylation, chromatin accessibility and G4 structure formation. Trained on A549 cell data, epiG4NN was then able to predict G4 formation in HEK293T and K562 cell lines. We observe the dependency of model performance with different epigenetic features on the underlying experimental condition of G4 detection. We expect that this approach will contribute to the systematic understanding of correlations between structural and epigenomic feature landscape.
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Affiliation(s)
- Anna Korsakova
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
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4
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Papp C, Mukundan VT, Jenjaroenpun P, Winnerdy FR, Ow GS, Phan AT, Kuznetsov VA. Stable bulged G-quadruplexes in the human genome: identification, experimental validation and functionalization. Nucleic Acids Res 2023; 51:4148-4177. [PMID: 37094040 DOI: 10.1093/nar/gkad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/23/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
DNA sequence composition determines the topology and stability of G-quadruplexes (G4s). Bulged G-quadruplex structures (G4-Bs) are a subset of G4s characterized by 3D conformations with bulges. Current search algorithms fail to capture stable G4-B, making their genome-wide study infeasible. Here, we introduced a large family of computationally defined and experimentally verified potential G4-B forming sequences (pG4-BS). We found 478 263 pG4-BS regions that do not overlap 'canonical' G4-forming sequences in the human genome and are preferentially localized in transcription regulatory regions including R-loops and open chromatin. Over 90% of protein-coding genes contain pG4-BS in their promoter or gene body. We observed generally higher pG4-BS content in R-loops and their flanks, longer genes that are associated with brain tissue, immune and developmental processes. Also, the presence of pG4-BS on both template and non-template strands in promoters is associated with oncogenesis, cardiovascular disease and stemness. Our G4-BS models predicted G4-forming ability in vitro with 91.5% accuracy. Analysis of G4-seq and CUT&Tag data strongly supports the existence of G4-BS conformations genome-wide. We reconstructed a novel G4-B 3D structure located in the E2F8 promoter. This study defines a large family of G4-like sequences, offering new insights into the essential biological functions and potential future therapeutic uses of G4-B.
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Affiliation(s)
- Csaba Papp
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Vineeth T Mukundan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Ghim Siong Ow
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Vladimir A Kuznetsov
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
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5
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Das P, Phan AT. Tetrad-binding ligands do not bind specifically to left-handed G-quadruplexes. Chem Commun (Camb) 2022; 58:11264-11267. [PMID: 36112098 DOI: 10.1039/d2cc03374g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-quadruplexes (G4s) are attractive anticancer targets. While right-handed G4s have been extensively investigated with many specific ligands reported, left-handed G4s formed by natural DNA have been recently discovered. Here we show that ligands specific for right-handed G4s, such as Phen-DC3 and RHAU peptide, do not bind specifically to left-handed G4s. In right-handed G4s, these ligands can displace capping overhangs and/or loops to stack on the exposed terminal tetrads. In contrast, the presence of tight T-capping in left-handed G4s hinders access to the tetrads.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore. .,NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
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6
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Chen H, Jayasinghe MK, Yeo EYM, Wu Z, Pirisinu M, Usman WM, Pham TT, Lim KW, Tran NV, Leung AYH, Du X, Zhang Q, Phan AT, Le MTN. CD33
‐targeting extracellular vesicles deliver antisense oligonucleotides against
FLT3‐ITD
and
miR
‐125b for specific treatment of acute myeloid leukaemia. Cell Prolif 2022; 55:e13255. [PMID: 35851970 PMCID: PMC9436904 DOI: 10.1111/cpr.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Acute Myeloid Leukaemia (AML) is the most common blood cancer in adults. Although 2 out of 3 AML patients go into total remission after chemotherapies and targeted therapies, the disease recurs in 60%–65% of younger adult patients within 3 years after diagnosis with a dramatically decreased survival rate. Therapeutic oligonucleotides are promising treatments under development for AML as they can be designed to silence oncogenes with high specificity and flexibility. However, there are not many well validated approaches for safely and efficiently delivering oligonucleotide drugs. This issue could be resolved by utilizing a new generation of delivery vehicles such as extracellular vesicles (EVs). Methods In this study, we harness red blood cell‐derived EVs (RBCEVs) and engineer them via exogenous drug loading and surface functionalization to develop an efficient drug delivery system for AML. Particularly, EVs are designed to target CD33, a common surface marker with elevated expression in AML cells via the conjugation of a CD33‐binding monoclonal antibody onto the EV surface. Results The conjugation of RBCEVs with the CD33‐binding antibody significantly increases the uptake of RBCEVs by CD33‐positive AML cells, but not by CD33‐negative cells. We also load CD33‐targeting RBCEVs with antisense oligonucleotides (ASOs) targeting FLT3‐ITD or miR‐125b, 2 common oncogenes in AML, and demonstrate that the engineered EVs improve leukaemia suppression in in vitro and in vivo models of AML. Conclusion Targeted RBCEVs represent an innovative, efficient, and versatile delivery platform for therapeutic ASOs and can expedite the clinical translation of oligonucleotide drugs for AML treatments by overcoming current obstacles in oligonucleotide delivery.
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Affiliation(s)
- Huan Chen
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Surgery, Immunology Program, Cancer Program and Nanomedicine Translational Program, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Hong Kong SAR
| | - Migara Kavishka Jayasinghe
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Surgery, Immunology Program, Cancer Program and Nanomedicine Translational Program, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
| | - Eric Yew Meng Yeo
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Surgery, Immunology Program, Cancer Program and Nanomedicine Translational Program, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
| | - Zhiyuan Wu
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Surgery, Immunology Program, Cancer Program and Nanomedicine Translational Program, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
| | - Marco Pirisinu
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Hong Kong SAR
| | - Waqas Muhammad Usman
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Hong Kong SAR
| | - Thach Tuan Pham
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Surgery, Immunology Program, Cancer Program and Nanomedicine Translational Program, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
| | - Kah Wai Lim
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences Nanyang Technological University Singapore Singapore
| | - Nhan Van Tran
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences Nanyang Technological University Singapore Singapore
| | - Anskar Y. H. Leung
- Department of Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital The University of Hong Kong Pok Fu Lam Hong Kong SAR
| | - Xin Du
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, Shenzhen Second People's Hospital The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine Shenzhen China
| | - Qiaoxia Zhang
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, Shenzhen Second People's Hospital The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine Shenzhen China
| | - Anh Tuân Phan
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences Nanyang Technological University Singapore Singapore
| | - Minh T. N. Le
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Department of Surgery, Immunology Program, Cancer Program and Nanomedicine Translational Program, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
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7
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Iyer VS, Boddul SV, Johnsson AK, Raposo B, Sharma RK, Shen Y, Kasza Z, Lim KW, Chemin K, Nilsson G, Malmström V, Phan AT, Wermeling F. Modulating T-cell activation with antisense oligonucleotides targeting lymphocyte cytosolic protein 2. J Autoimmun 2022; 131:102857. [PMID: 35780036 DOI: 10.1016/j.jaut.2022.102857] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022]
Abstract
Dysregulated T-cell activation is a hallmark of several autoimmune diseases such as rheumatoid arthritis (RA) and multiple sclerosis (MS). The lymphocyte cytosolic protein 2 (LCP2), also known as SLP-76, is essential for the development and activation of T cells. Despite the critical role of LCP2 in T-cell activation and the need for developing drugs that modify T-cell activation, no LCP2 inhibitors have been developed. This can be explained by the "undruggable" nature of LCP2, lacking a structure permissive to standard small molecule inhibitor modalities. Here, we explored an alternative drug modality, developing antisense oligonucleotides (ASOs) targeting LCP2 mRNAs, and evaluated its activity in modulating T-cell activation. We identified a set of 3' UTR targeting LCP2 ASOs, which knocked down LCP2 in a human T-cell line and primary human T cells and found that these suppressed T-cell receptor mediated activation. We also found that the ASOs suppressed FcεR1-mediated mast cell activation, in line with the role of LCP2 in mast cells. Taken together, our data provide examples of how immunomodulatory ASOs that interfere with undruggable targets can be developed and propose that such drug modalities can be used to treat autoimmune diseases.
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Affiliation(s)
- Vaishnavi Srinivasan Iyer
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Sanjaykumar V Boddul
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anna-Karin Johnsson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Bruno Raposo
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Ravi K Sharma
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yunbing Shen
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Zsolt Kasza
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Karine Chemin
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Nilsson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
| | - Fredrik Wermeling
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
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8
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Bose K, Maity A, Ngo KH, Vandana JJ, Shneider NA, Phan AT. Formation of RNA G-wires by G4C2 repeats associated with ALS and FTD. Biochem Biophys Res Commun 2022; 610:113-118. [DOI: 10.1016/j.bbrc.2022.03.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
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9
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Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT. Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex. Biochem Biophys Res Commun 2022; 613:153-158. [DOI: 10.1016/j.bbrc.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022]
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10
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Devi G, Winnerdy FR, Ang JCY, Lim KW, Phan AT. Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold. ACS Nano 2022; 16:533-540. [PMID: 34927423 DOI: 10.1021/acsnano.1c07630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.
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Affiliation(s)
- Gitali Devi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Jason Cheng Yu Ang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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11
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Abstract
G-quadruplex (G4) binding proteins regulate important biological processes, but their interaction networks are poorly understood. We report the first use of G4 as a warhead of a proteolysis-targeting chimera (G4-PROTAC) for targeted degradation of a G4-binding protein (RHAU/DHX36). G4-PROTAC provides a new way to explore G4-protein networks and to develop potential therapeutics.
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Affiliation(s)
- Kiran M Patil
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Danielle Chin
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Hui Ling Seah
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Qi Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore. .,NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
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12
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Chatain J, Blond A, Phan AT, Saintomé C, Alberti P. GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres. Nucleic Acids Res 2021; 49:7588-7601. [PMID: 34214172 PMCID: PMC8287962 DOI: 10.1093/nar/gkab518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson-Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.
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Affiliation(s)
- Jean Chatain
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
| | - Alain Blond
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d’Histoire naturelle, CNRS, Paris 75005, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Carole Saintomé
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
- Sorbonne Université, UFR927, Paris 75005, France
| | - Patrizia Alberti
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
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13
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Tan DJY, Cheong VV, Lim KW, Phan AT. A modular approach to enzymatic ligation of peptides and proteins with oligonucleotides. Chem Commun (Camb) 2021; 57:5507-5510. [PMID: 34036975 DOI: 10.1039/d1cc01348c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Joining peptides and oligonucleotides offers potential benefits, but current methods remain laborious. Here we present a novel approach towards enzymatic ligation of the two modalities through the development of tag phosphoramidites as adaptors that can be readily incorporated onto oligonucleotides. This simple and highly efficient approach paves the way towards streamlined development and production of peptide/protein-oligonucleotide conjugates.
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Affiliation(s)
- Derrick Jing Yang Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
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14
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Winnerdy FR, Bakalar B, Das P, Heddi B, Marchand A, Rosu F, Gabelica V, Phan AT. Unprecedented hour-long residence time of a cation in a left-handed G-quadruplex. Chem Sci 2021; 12:7151-7157. [PMID: 34123342 PMCID: PMC8153214 DOI: 10.1039/d1sc00515d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/06/2021] [Indexed: 11/21/2022] Open
Abstract
Cations are critical for the folding and assembly of nucleic acids. In G-quadruplex structures, cations can bind between stacked G-tetrads and coordinate with negatively charged guanine carbonyl oxygens. They usually exchange between binding sites and with the bulk in solution with time constants ranging from sub-millisecond to seconds. Here we report the first observation of extremely long-lived K+ and NH4 + ions, with an exchange time constant on the order of an hour, when coordinated at the center of a left-handed G-quadruplex DNA. A single-base mutation, that switched one half of the structure from left- to right-handed conformation resulting in a right-left hybrid G-quadruplex, was shown to remove this long-lived behaviour of the central cation.
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Affiliation(s)
- Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
- Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay Gif-sur-Yvette 91190 France
| | - Adrien Marchand
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB Pessac 33600 France
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie, Université de Bordeaux, CNRS & Inserm (IECB, UMS3033, US001) Pessac 33607 France
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB Pessac 33600 France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
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15
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Abstract
We generated a novel G-quadruplex (G4)-specific endonuclease by fusing a G4 recognition domain of the RHAU helicase with a cleavage domain of the Fok1 nuclease. The fusion protein can specifically bind a parallel G4 and cleave a double-stranded DNA (dsDNA) next to it. The new endonuclease could be used to detect a G4 in a long dsDNA, providing a useful tool for mapping the formation of G4s in the genome.
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Affiliation(s)
- Dung Thanh Dang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.
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16
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Maity A, Winnerdy FR, Chen G, Phan AT. Duplexes Formed by G 4C 2 Repeats Contain Alternate Slow- and Fast-Flipping G·G Base Pairs. Biochemistry 2021; 60:1097-1107. [PMID: 33750098 DOI: 10.1021/acs.biochem.0c00916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Aberrant expansion of the hexanucleotide GGGGCC (or G4C2) repeat in the human C9ORF72 gene is the most common genetic factor found behind amyotrophic lateral sclerosis and frontotemporal dementia. The hypothesized pathways, through which the repeat expansions contribute to the pathology, involve one or more secondary structural forms of the DNA and/or RNA sequences, such as G-quadruplexes, duplexes, and hairpins. Here, we study the structures of DNA and RNA duplexes formed by G4C2 repeats, which contain G(syn)·G(anti) base pairs flanked by either G·C or C·G base pairs. We show that duplexes formed by G4C2 repeats contain alternately two types of G·G pair contexts exhibiting different syn-anti base flipping dynamics (∼100 ms vs ∼2 ms for DNA and ∼50 ms vs ∼20 ms for RNA at 10 °C, respectively) depending on the flanking bases, with the slow-flipping G·G pairs being flanked by a guanine at the 5'-end and the fast-flipping G·G pairs being flanked by a cytosine at the 5'-end. Our findings on the structures and dynamics of G·G base pairs in DNA and RNA duplexes formed by G4C2 repeats provide a foundation for further studies of the functions and targeting of such biologically relevant motifs.
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Affiliation(s)
- Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Gang Chen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), No. 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P. R. China
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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17
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Seviour T, Winnerdy FR, Wong LL, Shi X, Mugunthan S, Foo YH, Castaing R, Adav SS, Subramoni S, Kohli GS, Shewan HM, Stokes JR, Rice SA, Phan AT, Kjelleberg S. The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures. NPJ Biofilms Microbiomes 2021; 7:27. [PMID: 33741996 PMCID: PMC7979868 DOI: 10.1038/s41522-021-00197-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/12/2021] [Indexed: 12/31/2022] Open
Abstract
Extracellular DNA, or eDNA, is recognised as a critical biofilm component; however, it is not understood how it forms networked matrix structures. Here, we isolate eDNA from static-culture Pseudomonas aeruginosa biofilms using ionic liquids to preserve its biophysical signatures of fluid viscoelasticity and the temperature dependency of DNA transitions. We describe a loss of eDNA network structure as resulting from a change in nucleic acid conformation, and propose that its ability to form viscoelastic structures is key to its role in building biofilm matrices. Solid-state analysis of isolated eDNA, as a proxy for eDNA structure in biofilms, reveals non-canonical Hoogsteen base pairs, triads or tetrads involving thymine or uracil, and guanine, suggesting that the eDNA forms G-quadruplex structures. These are less abundant in chromosomal DNA and disappear when eDNA undergoes conformation transition. We verify the occurrence of G-quadruplex structures in the extracellular matrix of intact static and flow-cell biofilms of P. aeruginosa, as displayed by the matrix to G-quadruplex-specific antibody binding, and validate the loss of G-quadruplex structures in vivo to occur coincident with the disappearance of eDNA fibres. Given their stability, understanding how extracellular G-quadruplex structures form will elucidate how P. aeruginosa eDNA builds viscoelastic networks, which are a foundational biofilm property.
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Affiliation(s)
- Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore. .,WATEC Aarhus University Centre for Water Technology, Aarhus, Denmark.
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Remi Castaing
- Materials and Chemical Characterisation Facility (MC2), University of Bath, Bath, UK
| | - Sunil S Adav
- Singapore Phenome Centre, Nanyang Technological University, Singapore, Singapore
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Gurjeet Singh Kohli
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Heather M Shewan
- School of Chemical Engineering, University of Queensland, Brisbane, QLD, Australia
| | - Jason R Stokes
- School of Chemical Engineering, University of Queensland, Brisbane, QLD, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,The iThree Institute, University of Technology Sydney, Sydney, NSW, Australia.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore. .,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. .,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.
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18
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Abstract
A recent study on the left-handed G-quadruplex (LHG4) DNA revealed a 12-nt minimal motif GTGGTGGTGGTG with the ability to independently form an LHG4 and to drive an adjacent sequence to LHG4 formation. Here we have identified a second LHG4-forming motif, GGTGGTGGTGTG, and determined the X-ray crystal structure of an LHG4 involving this motif. Our structural analysis indicated the role of split guanines and single thymine loops in promoting LHG4 formation.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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19
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Das P, Ngo KH, Winnerdy FR, Maity A, Bakalar B, Mechulam Y, Schmitt E, Phan AT. Bulges in left-handed G-quadruplexes. Nucleic Acids Res 2021; 49:1724-1736. [PMID: 33503265 PMCID: PMC7897477 DOI: 10.1093/nar/gkaa1259] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/03/2022] Open
Abstract
G-quadruplex (G4) DNA structures with a left-handed backbone progression have unique and conserved structural features. Studies on sequence dependency of the structures revealed the prerequisites and some minimal motifs required for left-handed G4 formation. To extend the boundaries, we explore the adaptability of left-handed G4s towards the existence of bulges. Here we present two X-ray crystal structures and an NMR solution structure of left-handed G4s accommodating one, two and three bulges. Bulges in left-handed G4s show distinct characteristics as compared to those in right-handed G4s. The elucidation of intricate structural details will help in understanding the possible roles and limitations of these unique structures.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Khac Huy Ngo
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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20
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Tran NV, Nguyen LTA, Lim KW, Phan AT. Potent and Selective Knockdown of Tyrosine Kinase 2 by Antisense Oligonucleotides. Immunohorizons 2021; 5:70-80. [PMID: 33542028 DOI: 10.4049/immunohorizons.2000108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 11/19/2022] Open
Abstract
Tyrosine kinase 2 (TYK2) is a member of the JAK family of nonreceptor tyrosine kinase, together with JAK1, JAK2, and JAK3. JAKs are important signaling mediators of many proinflammatory cytokines and represent compelling pharmacological targets for autoimmune and inflammatory diseases. Pan-acting small-molecule JAK inhibitors were approved for the treatment of rheumatoid arthritis and ulcerative colitis. However, their limited selectivity among JAK members have led to undesirable side effects, driving a search toward specific JAK inhibitors. Recently, TYK2 has emerged as a target of choice for the treatment of autoimmune diseases and severe COVID-19 with an optimum balance between efficacy and safety, based on observations from human genetics studies and clinical outcomes of several agents targeting cytokine pathways for which TYK2 plays an essential role. In this article, we address selective targeting of TYK2 from the genetic sequence space through development of antisense oligonucleotides (ASOs) against TYK2 mRNA. Potent ASO candidates were identified from the screening of over 200 ASOs using locked nucleic acid gapmer design. The lead ASOs exhibited potent and selective knockdown of TYK2 mRNA and protein across a panel of model human cell lines in a dose-dependent manner, showing no reduction in the mRNA and protein expression levels of other JAK paralogs. In agreement with the depletion of TYK2 proteins, several TYK2-mediated cytokine signaling pathways, including IFN-α and IL-12, were inhibited upon ASO treatment. Our results established the TYK2 ASOs as investigational tool compound and potential therapeutic agent for the treatment of autoimmune diseases and severe COVID-19.
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Affiliation(s)
- Nhan Van Tran
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; and
| | - Le Tuan Anh Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; and
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; and
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; and .,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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21
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Tan DJY, Das P, Winnerdy FR, Lim KW, Phan AT. Guanine anchoring: a strategy for specific targeting of a G-quadruplex using short PNA, LNA and DNA molecules. Chem Commun (Camb) 2021; 56:5897-5900. [PMID: 32338660 DOI: 10.1039/d0cc01778g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Two separate structural elements of a G-quadruplex (G4), a vacant site and a flanking single-strand, provide an opportunity for specific targeting of a particular G4 structure via dual recognition. Here, we show that a short peptide nucleic acid (PNA) can specifically recognize and bind to a G4 at sub-micromolar affinity based on both G-tetrad vacant site filling and complementary duplex formation. This sequence-guided guanine-anchoring strategy can be further developed for specific targeting of G4 structures using short DNA, LNA and PNA strands.
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Affiliation(s)
- Derrick Jing Yang Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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22
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Tan DJY, Winnerdy FR, Lim KW, Phan AT. Coexistence of two quadruplex-duplex hybrids in the PIM1 gene. Nucleic Acids Res 2020; 48:11162-11171. [PMID: 32976598 PMCID: PMC7641742 DOI: 10.1093/nar/gkaa752] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
The triple-negative breast cancer (TNBC), a subtype of breast cancer which lacks of targeted therapies, exhibits a poor prognosis. It was shown recently that the PIM1 oncogene is highly related to the proliferation of TNBC cells. A quadruplex-duplex hybrid (QDH) forming sequence was recently found to exist near the transcription start site of PIM1. This structure could be an attractive target for regulation of the PIM1 gene expression and thus the treatment of TNBC. Here, we present the solution structures of two QDHs that could coexist in the human PIM1 gene. Form 1 is a three-G-tetrad-layered (3+1) G-quadruplex containing a propeller loop, a lateral loop and a stem-loop made up of three G•C Watson-Crick base pairs. On the other hand, Form 2 is an anti-parallel G-quadruplex comprising two G-tetrads and a G•C•G•C tetrad; the structure has three lateral loops with the middle stem-loop made up of two Watson-Crick G•C base pairs. These structures provide valuable information for the design of G-quadruplex-specific ligands for PIM1 transcription regulation.
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Affiliation(s)
- Derrick J Y Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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23
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Ngoc Nguyen TQ, Lim KW, Phan AT. Duplex formation in a G-quadruplex bulge. Nucleic Acids Res 2020; 48:10567-10575. [PMID: 32960213 PMCID: PMC7544226 DOI: 10.1093/nar/gkaa738] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 01/05/2023] Open
Abstract
Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex–duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.
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Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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24
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Yaneva MY, Cheong VV, Cheng JK, Lim KW, Phan AT. Stapling a G-quadruplex specific peptide. Biochem Biophys Res Commun 2020; 531:62-66. [DOI: 10.1016/j.bbrc.2020.02.144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/22/2020] [Indexed: 12/12/2022]
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25
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Nguyen TQN, Tooh YW, Sugiyama R, Nguyen TPD, Purushothaman M, Leow LC, Hanif K, Yong RHS, Agatha I, Winnerdy FR, Gugger M, Phan AT, Morinaka BI. Post-translational formation of strained cyclophanes in bacteria. Nat Chem 2020; 12:1042-1053. [DOI: 10.1038/s41557-020-0519-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/04/2020] [Indexed: 11/09/2022]
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26
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Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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27
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Maity A, Winnerdy FR, Chang WD, Chen G, Phan AT. Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs. Nucleic Acids Res 2020; 48:3315-3327. [PMID: 32100003 PMCID: PMC7102960 DOI: 10.1093/nar/gkaa008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
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Affiliation(s)
- Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Weili Denyse Chang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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28
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Ngo KH, Yang R, Das P, Nguyen GKT, Lim KW, Tam JP, Wu B, Phan AT. Cyclization of a G4-specific peptide enhances its stability and G-quadruplex binding affinity. Chem Commun (Camb) 2020; 56:1082-1084. [DOI: 10.1039/c9cc06748e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Head-to-tail cyclization of a G-quadruplex-specific peptide was shown to enhance its stability and G-quadruplex binding affinity.
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Affiliation(s)
- Khac Huy Ngo
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - Renliang Yang
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Poulomi Das
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | | | - Kah Wai Lim
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - James P. Tam
- School of Biological Sciences
- Nanyang Technological University
- Singapore
- NTU Institute of Structural Biology
- Nanyang Technological University
| | - Bin Wu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
- NTU Institute of Structural Biology
- Nanyang Technological University
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
- NTU Institute of Structural Biology
- Nanyang Technological University
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29
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Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan AT. Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex. J Struct Biol 2020; 209:107399. [DOI: 10.1016/j.jsb.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022]
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30
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Winnerdy FR, Das P, Heddi B, Phan AT. Solution Structures of a G-Quadruplex Bound to Linear- and Cyclic-Dinucleotides. J Am Chem Soc 2019; 141:18038-18047. [PMID: 31661272 DOI: 10.1021/jacs.9b05642] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyclic dinucleotides have emerged as important secondary messengers and cell signaling molecules that regulate several cell responses. A guanine-deficit G-quadruplex structure formation by a sequence containing (4n - 1) guanines, n denoting the number of G-tetrad layers, was previously reported. Here, a (4n - 1) G-quadruplex structure is shown to be capable of binding guanine-containing dinucleotides in micromolar affinity. The guanine base of the dinucleotides interacts with a vacant G-triad, forming four additional Hoogsteen hydrogen bonds to complete a G-tetrad. Solution structures of two complexes, both comprised of a (4n - 1) G-quadruplex structure, one bound to a linear dinucleotide (d(AG)) and the other to a cyclic dinucleotide (cGAMP), are solved using NMR spectroscopy. The latter suggests sufficiently strong interaction between the guanine base of the dinucleotide and the vacant G-triad, which acts as an anchor point of binding. The binding interfaces from the two solution structures provide useful information for specific ligand design. The results also infer that other guanine-containing metabolites of a similar size have the capability of binding G-quadruplexes, potentially affecting the expression of the metabolites and functionality of the bound G-quadruplexes.
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Affiliation(s)
- Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Poulomi Das
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore.,Laboratoire de Biologie et de Pharmacologie Appliquée , CNRS UMR 8113 , Ecole Normale Supérieure Paris-Saclay , Cachan 94235 , France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , Singapore 636921 , Singapore
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31
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Affiliation(s)
- Thi Hong Anh Truong
- School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
- NTU Institute of Structural BiologyNanyang Technological University Singapore 636921 Singapore
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32
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Affiliation(s)
- Thi Hong Anh Truong
- School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
- NTU Institute of Structural BiologyNanyang Technological University Singapore 636921 Singapore
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33
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Winnerdy FR, Bakalar B, Maity A, Vandana JJ, Mechulam Y, Schmitt E, Phan AT. NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes. Nucleic Acids Res 2019; 47:8272-8281. [PMID: 31216034 PMCID: PMC6735952 DOI: 10.1093/nar/gkz349] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/16/2019] [Accepted: 06/13/2019] [Indexed: 01/29/2023] Open
Abstract
Analogous to the B- and Z-DNA structures in double-helix DNA, there exist both right- and left-handed quadruple-helix (G-quadruplex) DNA. Numerous conformations of right-handed and a few left-handed G-quadruplexes were previously observed, yet they were always identified separately. Here, we present the NMR solution and X-ray crystal structures of a right- and left-handed hybrid G-quadruplex. The structure reveals a stacking interaction between two G-quadruplex blocks with different helical orientations and displays features of both right- and left-handed G-quadruplexes. An analysis of loop mutations suggests that single-nucleotide loops are preferred or even required for the left-handed G-quadruplex formation. The discovery of a right- and left-handed hybrid G-quadruplex further expands the polymorphism of G-quadruplexes and is potentially useful in designing a left-to-right junction in G-quadruplex engineering.
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Affiliation(s)
- Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - J Jeya Vandana
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, Palaiseau 91128, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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34
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Pathak P, Yao W, Hook KD, Vik R, Winnerdy FR, Brown JQ, Gibb BC, Pursell ZF, Phan AT, Jayawickramarajah J. Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns. J Am Chem Soc 2019; 141:12582-12591. [PMID: 31322869 DOI: 10.1021/jacs.9b03250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.
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Affiliation(s)
- Pravin Pathak
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Wei Yao
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Katherine Delaney Hook
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Ryan Vik
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Jonathon Quincy Brown
- Department of Biomedical Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Bruce C Gibb
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Janarthanan Jayawickramarajah
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
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35
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Sengar A, Vandana J, Chambers VS, Di Antonio M, Winnerdy F, Balasubramanian S, Phan AT. Structure of a (3+1) hybrid G-quadruplex in the PARP1 promoter. Nucleic Acids Res 2019; 47:1564-1572. [PMID: 30551210 PMCID: PMC6379715 DOI: 10.1093/nar/gky1179] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/02/2018] [Accepted: 12/12/2018] [Indexed: 01/08/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) has emerged as an attractive target for cancer therapy due to its key role in DNA repair processes. Inhibition of PARP1 in BRCA-mutated cancers has been observed to be clinically beneficial. Recent genome-mapping experiments have identified a non-canonical G-quadruplex-forming sequence containing bulges within the PARP1 promoter. Structural features, like bulges, provide opportunities for selective chemical targeting of the non-canonical G-quadruplex structure within the PARP1 promoter, which could serve as an alternative therapeutic approach for the regulation of PARP1 expression. Here we report the G-quadruplex structure formed by a 23-nucleotide G-rich sequence in the PARP1 promoter. Our study revealed a three-layered intramolecular (3+1) hybrid G-quadruplex scaffold, in which three strands are oriented in one direction and the fourth in the opposite direction. This structure exhibits unique structural features such as an adenine bulge and a G·G·T base triple capping structure formed between the central edgewise loop, propeller loop and 5' flanking terminal. Given the highly important role of PARP1 in DNA repair and cancer intervention, this structure presents an attractive opportunity to explore the therapeutic potential of PARP1 inhibition via G-quadruplex DNA targeting.
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Affiliation(s)
- Anjali Sengar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - J Jeya Vandana
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Vicki S Chambers
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Marco Di Antonio
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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36
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Affiliation(s)
- Blaž Bakalar
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS; Ecole Normale Supérieure Paris-Saclay; 94235 Cachan France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS; Ecole Polytechnique; 91128 Palaiseau France
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS; Ecole Polytechnique; 91128 Palaiseau France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
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37
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Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT. A Minimal Sequence for Left-Handed G-Quadruplex Formation. Angew Chem Int Ed Engl 2019; 58:2331-2335. [PMID: 30481397 DOI: 10.1002/anie.201812628] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Indexed: 12/20/2022]
Abstract
Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X-ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left-handed DNA G-quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left-handed G-quadruplex formation.
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Affiliation(s)
- Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay, 94235, Cachan, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
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38
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Ma Y, Iida K, Sasaki S, Hirokawa T, Heddi B, Phan AT, Nagasawa K. Synthesis and Telomeric G-Quadruplex-Stabilizing Ability of Macrocyclic Hexaoxazoles Bearing Three Side Chains. Molecules 2019; 24:molecules24020263. [PMID: 30642002 PMCID: PMC6358838 DOI: 10.3390/molecules24020263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 01/02/2023] Open
Abstract
G-quadruplexes (G4s), which are structures formed in guanine-rich regions of DNA, are involved in a variety of significant biological functions, and therefore “sequence-dependent” selective G4-stabilizing agents are required as tools to investigate and modulate these functions. Here, we describe the synthesis of a new series of macrocyclic hexaoxazole-type G4 ligand (6OTD) bearing three side chains. One of these ligands, 5b, stabilizes telomeric G4 preferentially over the G4-forming DNA sequences of c-kit and K-ras, due to the interaction of its piperazinylalkyl side chain with the groove of telomeric G4.
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Affiliation(s)
- Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan.
| | - Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Takatsugu Hirokawa
- Transborder Medical Reserch Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
- Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo 135-0064, Japan.
| | - Brahim Heddi
- Laboratoire de Biologie et Pharmacologie appliquée, CNRS UMR 8113, ENS paris-saclay 60 avenue du president Wilson, 94230 Cachan, France.
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore 637371, Singapore.
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore 637371, Singapore.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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39
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Nadai M, Doria F, Scalabrin M, Pirota V, Grande V, Bergamaschi G, Amendola V, Winnerdy FR, Phan AT, Richter SN, Freccero M. A Catalytic and Selective Scissoring Molecular Tool for Quadruplex Nucleic Acids. J Am Chem Soc 2018; 140:14528-14532. [PMID: 30351011 PMCID: PMC6242190 DOI: 10.1021/jacs.8b05337] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A copper complex embedded in the structure of a water-soluble naphthalene diimide has been designed to bind and cleave G-quadruplex DNA. We describe the properties of this ligand, including its catalytic activity in the generation of ROS. FRET melting, CD, NMR, gel sequencing, and mass spectrometry experiments highlight a unique and unexpected selectivity in cleaving G-quadruplex sequences. This selectivity relies both on the binding affinity and structural features of the targeted G-quadruplexes.
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Affiliation(s)
- Matteo Nadai
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Filippo Doria
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Valentina Pirota
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Vincenzo Grande
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Greta Bergamaschi
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Valeria Amendola
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Sara N Richter
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Mauro Freccero
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
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40
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Sedghi Masoud S, Yamaoki Y, Ma Y, Marchand A, Winnerdy FR, Gabelica V, Phan AT, Katahira M, Nagasawa K. Analysis of Interactions between Telomeric i-Motif DNA and a Cyclic Tetraoxazole Compound. Chembiochem 2018; 19:2268-2272. [PMID: 30160816 DOI: 10.1002/cbic.201800425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Indexed: 12/31/2022]
Abstract
The interaction of a macrocyclic tetraoxazole compound, L2H2-4OTD (1), with two aminoalkyl side chains and telomeric i-motif, was investigated by means of electrophoretic mobility shift assay, circular dichroism spectroscopy, mass spectrometry and NMR spectroscopy analyses. The results indicate that 1 interacts with the i-motif structure at two preferred binding sites.
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Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Yudai Yamaoki
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yue Ma
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Adrien Marchand
- Université de Bordeaux, INSERM, CNRS, Acides Nucléiques, Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, SPMS PAP 05-04, 637371, Singapore, Singapore
| | - Valérie Gabelica
- Université de Bordeaux, INSERM, CNRS, Acides Nucléiques, Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, SPMS PAP 05-04, 637371, Singapore, Singapore
| | - Masato Katahira
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
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41
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Butovskaya E, Heddi B, Bakalar B, Richter SN, Phan AT. Major G-Quadruplex Form of HIV-1 LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop. J Am Chem Soc 2018; 140:13654-13662. [PMID: 30299955 PMCID: PMC6202629 DOI: 10.1021/jacs.8b05332] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Nucleic
acids can form noncanonical four-stranded structures called
G-quadruplexes. G-quadruplex-forming sequences are found in several
genomes including human and viruses. Previous studies showed that
the G-rich sequence located in the U3 promoter region of the HIV-1
long terminal repeat (LTR) folds into a set of dynamically interchangeable
G-quadruplex structures. G-quadruplexes formed in the LTR could act
as silencer elements to regulate viral transcription. Stabilization
of LTR G-quadruplexes by G-quadruplex-specific ligands resulted in
decreased viral production, suggesting the possibility of targeting
viral G-quadruplex structures for antiviral purposes. Among all the
G-quadruplexes formed in the LTR sequence, LTR-III was shown to be the major G-quadruplex conformation in vitro. Here we report the NMR structure of LTR-III in K+ solution, revealing the formation of a unique quadruplex–duplex
hybrid consisting of a three-layer (3 + 1) G-quadruplex scaffold,
a 12-nt diagonal loop containing a conserved duplex-stem, a 3-nt lateral
loop, a 1-nt propeller loop, and a V-shaped loop. Our structure showed
several distinct features including a quadruplex–duplex junction,
representing an attractive motif for drug targeting. The structure
solved in this study may be used as a promising target to selectively
impair the viral cycle.
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Affiliation(s)
- Elena Butovskaya
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore.,Department of Molecular Medicine , University of Padua , Padua 35121 , Italy
| | - Brahim Heddi
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, École Normale Supérieure Paris-Saclay , Cachan 94235 , France
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Sara N Richter
- Department of Molecular Medicine , University of Padua , Padua 35121 , Italy
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
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42
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Abstract
We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure. DNA and RNA G-quadruplexes can stack to form higher-order structures called G-wires. Here the authors report high-resolution AFM images of higher-order DNA G-quadruplexes in aqueous solution that could impact the design of G-wire based nanodevices and the understanding of G-wires in biology.
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Affiliation(s)
- Krishnashish Bose
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Christopher J Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Brahim Heddi
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure, Paris-Saclay, France
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
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43
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Asamitsu S, Obata S, Phan AT, Hashiya K, Bando T, Sugiyama H. Simultaneous Binding of Hybrid Molecules Constructed with Dual DNA-Binding Components to a G-Quadruplex and Its Proximal Duplex. Chemistry 2018; 24:4428-4435. [DOI: 10.1002/chem.201705945] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Shunsuke Obata
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Kaori Hashiya
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS); Kyoto University, Sakyo; Kyoto 606-8501 Japan
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44
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Lech CJ, Phan AT. Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification. Nucleic Acids Res 2017; 45:6265-6274. [PMID: 28499037 PMCID: PMC5499775 DOI: 10.1093/nar/gkx243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0–13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin–avidin conjugation approach.
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Affiliation(s)
- Christopher Jacques Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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45
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Do NQ, Chung WJ, Truong THA, Heddi B, Phan AT. G-quadruplex structure of an anti-proliferative DNA sequence. Nucleic Acids Res 2017; 45:7487-7493. [PMID: 28549181 PMCID: PMC5499593 DOI: 10.1093/nar/gkx274] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/24/2017] [Indexed: 01/06/2023] Open
Abstract
AGRO100 (also known as AS1411) is a G-rich oligonucleotide that has long been established as a potent anti-cancer aptamer. However, the structure of AGRO100 remained unresolved, due to the co-existence of multiple different G-quadruplex conformations. We identified a DNA sequence named AT11, derived from AGRO100, which formed a single major G-quadruplex conformation and exhibited a similar anti-proliferative activity as AGRO100. The solution structure of AT11 revealed a four-layer G-quadruplex comprising of two propeller-type parallel-stranded subunits connected through a central linker. The stacking between the two subunits occurs at the 3΄-end of the first block and the 5΄-end of the second block. The structure of the anti-proliferative DNA sequence AT11 will allow greater understanding on the G-quadruplex folding principles and aid in structural optimization of anti-proliferative oligonucleotides.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences.,School of Biological Sciences, Nanyang Technological University, Singapore
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46
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Nguyen TQN, Lim KW, Phan AT. A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs. Sci Rep 2017; 7:11969. [PMID: 28931822 PMCID: PMC5607247 DOI: 10.1038/s41598-017-10583-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022] Open
Abstract
Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements. Such a dual-specific targeting strategy would combine the sequence specificity of duplex-binders and the strong binding affinity of quadruplex-binders, potentially allowing the specific targeting of unique quadruplex structures. Future research can be directed towards the development of conjugated compounds targeting specific genomic quadruplex-duplex sites, for which the linker would be highly context-dependent in terms of length and flexibility, as well as the attachment points onto both ligands.
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Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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47
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Adrian M, Winnerdy FR, Heddi B, Phan AT. Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding. Biophys J 2017; 113:775-784. [PMID: 28834714 DOI: 10.1016/j.bpj.2017.05.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/25/2022] Open
Abstract
Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.
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Affiliation(s)
- Michael Adrian
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Brahim Heddi
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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48
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49
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De Nicola B, Lech CJ, Heddi B, Regmi S, Frasson I, Perrone R, Richter SN, Phan AT. Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome. Nucleic Acids Res 2016; 44:6442-51. [PMID: 27298260 PMCID: PMC5291261 DOI: 10.1093/nar/gkw432] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
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Affiliation(s)
- Beatrice De Nicola
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore Department of Molecular Medicine, University of Padua, Italy
| | - Christopher J Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Sagar Regmi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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50
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Abstract
Abstract The i-motif is an intercalated structure formed by association in a head to tail orientation of two parallel duplexes whose strands are held together by hemiprotonated C·C(+) pairs. The i-motif may be formed by a single strand containing four cytidine repeats, by association of two strands containing two cytidine repeats or by four strands containing a single cytidine stretch. The repeated C-rich sequences of centromeric and telomeric regions can potentially fold into an intramolecular i-motif. We have investigated by NMR spectroscopy the structure of d(CCCTA(2)CCCTA(2)CCCTA(2)CCCT), a fragment of the vertebrate telomere. It includes an i-motif core of six intercalated C·C(+) pairs. At one end (the "top"), the central TA(2) linker loops across one of the narrow grooves, and the core is extended by base stacking in the loop. At the bottom, where the two other TA(2) linkers loop across the wide grooves, the NMR spectra reveal motions in the microsecond to millisecond scale. The pseudo-symmetry of the structure, which results in degenerate spectra and poor resolution, was broken by appropriate substitution of T by U and of C by 5-methylcytidine (5mC). This allowed us to solve the structure of d(CCCTA(2)5mCCCTA(2)CCCUA(2)CCCT). The motion is restricted to a flip of A18 around the glycosidic bond. Returning to the pseudo-symmetrical sequence, we find that each of the bottom loops switches between the structures of the first and third loops of the non-symmetrical sequence. We also analyzed the effects of the loop sequence and of the length of the C-stretches on the topology and stability of the intramolecular i-motif structure.
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Affiliation(s)
- A T Phan
- a Groupe de Biophysique de l'Ecole Polytechnique et de l'UMR 7643 du CNRS , 91128 , Palaiseau , France
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