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Jiao Z, Zhang X, Chen W, Guo Z, Huang B, Ru J, Huang X, Liu J. Highly-Selective fluorescent Fe 3O 4@PPy aptasensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124447. [PMID: 38761471 DOI: 10.1016/j.saa.2024.124447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
Label-free nucleic acid fluorescent probes are gaining popularity due to their low cost and ease of application. However, the primary challenges associated with label-free fluorescent probes stem from their tendency to interact with other biomolecules, such as RNA, proteins, and enzymes, which results in low specificity. In this work, we have developed a simple detection platform that utilizes Fe3O4@PPy in combination with a label-free nucleic acid probe, 1,1,2,2-tetrakis[4-(2-bromo-ethoxy)phenyl]ethene (TTAPE) or Malachite Green (MG), for highly selective detection of metal ions, acetamiprid, and thrombin. Fe3O4@PPy not only adsorbs aptamers through electrostatic interactions, π-π bonding, and hydrogen bonding, but also quenches the fluorescence of the TTAPE/MG. Upon the addition of target compounds, the aptasensor separates from Fe3O4@PPy through magnetic separation. Moreover, by changing different aptamers, the aptasensor was applied to detect metal ions, acetamiprid, and thrombin, with the turned-on photoluminescence (PL) emission intensity recorded and showing linearity to the concentrations of targets. The robustness of method was demonstrated by applying it to real samples, which included vegetables (for detecting acetamiprid with LODs of 0.02 and 0.04 ng/L), serum samples (for detecting thrombin with LODs of 5.5 and 4.3 nM), and water samples (for detecting Pb2+ with an LOD of 0.17 nM). Therefore, due to its impressive selectivity and sensitivity, the Fe3O4@PPy aptasensor could be utilized as a universal detection platform for various clinical and environmental applications.
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Affiliation(s)
- Zhe Jiao
- School of Environment and Civil Engineering, Dongguan Key Laboratory of Low-carbon and Recycling, Dongguan University of Technology, Dongguan 523808, China.
| | - Xiaolin Zhang
- School of Environment and Civil Engineering, Dongguan Key Laboratory of Low-carbon and Recycling, Dongguan University of Technology, Dongguan 523808, China
| | - Weibin Chen
- School of Environment and Civil Engineering, Dongguan Key Laboratory of Low-carbon and Recycling, Dongguan University of Technology, Dongguan 523808, China
| | - Zongning Guo
- Guangdong Provincial Key Laboratory of Intelligent Port Security Inspection, Guangzhou 510700, China; Huangpu Customs District Technology Center, Dongguan 523000, China
| | - Binyu Huang
- Guangdong Provincial Key Laboratory of Intelligent Port Security Inspection, Guangzhou 510700, China
| | - Jiantao Ru
- School of Environment and Civil Engineering, Dongguan Key Laboratory of Low-carbon and Recycling, Dongguan University of Technology, Dongguan 523808, China
| | - Xuelin Huang
- Guangdong Provincial Key Laboratory of Intelligent Port Security Inspection, Guangzhou 510700, China; Huangpu Customs District Technology Center, Dongguan 523000, China.
| | - Jinbin Liu
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China.
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2
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Iachettini S, Biroccio A, Zizza P. Therapeutic Use of G4-Ligands in Cancer: State-of-the-Art and Future Perspectives. Pharmaceuticals (Basel) 2024; 17:771. [PMID: 38931438 PMCID: PMC11206494 DOI: 10.3390/ph17060771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
G-quadruplexes (G4s) are guanine-rich non-canonical secondary structures of nucleic acids that were identified in vitro almost half a century ago. Starting from the early 1980s, these structures were also observed in eukaryotic cells, first at the telomeric level and later in regulatory regions of cancer-related genes, in regulatory RNAs and within specific cell compartments such as lysosomes, mitochondria, and ribosomes. Because of the involvement of these structures in a large number of biological processes and in the pathogenesis of several diseases, including cancer, the interest in G4 targeting has exponentially increased in the last few years, and a great number of novel G4 ligands have been developed. Notably, G4 ligands represent a large family of heterogeneous molecules that can exert their functions by recognizing, binding, and stabilizing G4 structures in multiple ways. Regarding anti-cancer activity, the efficacy of G4 ligands was originally attributed to the capability of these molecules to inhibit the activity of telomerase, an enzyme that elongates telomeres and promotes endless replication in cancer cells. Thereafter, novel mechanisms through which G4 ligands exert their antitumoral activities have been defined, including the induction of DNA damage, control of gene expression, and regulation of metabolic pathways, among others. Here, we provided a perspective on the structure and function of G4 ligands with particular emphasis on their potential role as antitumoral agents. In particular, we critically examined the problems associated with the clinical translation of these molecules, trying to highlight the main aspects that should be taken into account during the phases of drug design and development. Indeed, taking advantage of the successes and failures, and the more recent technological progresses in the field, it would be possible to hypothesize the development of these molecules in the future that would represent a valid option for those cancers still missing effective therapies.
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Affiliation(s)
| | | | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS—Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Roma, Italy; (S.I.); (A.B.)
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3
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Anil A, Chaskar J, Pawar AB, Tiwari A, Chaskar AC. Recent advances in DNA-based probes for photoacoustic imaging. J Biotechnol 2024; 382:8-20. [PMID: 38211667 DOI: 10.1016/j.jbiotec.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
Photoacoustic imaging(PAI) is a widely developing imaging modality that has seen tremendous evolvement in the last decade. PAI has gained the upper hand in the imaging field as it takes advantage of optical absorption and ultrasound detection that imparts higher resolution, rich contrast and elevated penetration depth. Unlike other imaging techniques, PAI does not use ionising radiation and is a better, cost-effective and healthier alternative to other imaging techniques. It offers greater specificity than conventional ultrasound imaging with the ability to detect haemoglobin, lipids, water and other light-absorbing chromophores. These properties of PAI have led to its extended applications in the biomedical field in the treatment of diseases such as cancer. This paper reviews how DNA probes have been used in PAI, the various techniques by which it has been modified, and their role in the process. We also focus on different nanocomposites containing DNA having PAI and photothermal therapy(PTT) properties for detection, diagnosis and therapy, its constituents and the role of DNA in it.
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Affiliation(s)
- Anusri Anil
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India
| | - Jyotsna Chaskar
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India
| | - Avinash B Pawar
- Department of Chemistry, Bharati Vidyapeeth (Deemed to be University), Yashwantrao Mohite College of Arts, Science & Commerce, Pune 411038, India
| | - Abhishekh Tiwari
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India.
| | - Atul Changdev Chaskar
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India; Department of Chemistry, Institute of Chemical Technology, Mumbai.
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4
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Lopina OD, Sidorenko SV, Fedorov DA, Klimanova EA. G-Quadruplexes as Sensors of Intracellular Na+/K + Ratio: Potential Role in Regulation of Transcription and Translation. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S262-S277. [PMID: 38621755 DOI: 10.1134/s0006297924140153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 04/17/2024]
Abstract
Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.
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Affiliation(s)
- Olga D Lopina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | | | - Dmitry A Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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5
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Schult P, Paeschke K. In-gel staining methods of G4 DNA and RNA structures. Methods Enzymol 2023; 695:29-43. [PMID: 38521589 DOI: 10.1016/bs.mie.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplexes (G4) are functionally important nucleic acid structures, involved in many cellular pathways. They are often dynamically regulated in cells, which makes detecting them in vivo challenging and dependent on sophisticated technical equipment. Therefore, in vitro studies are commonly performed as a first step to confirm a candidate sequence folds into a G4. Several methods have been developed, each with its individual pros and cons. A highly accessible and quick approach, without the need for specialized equipment, is the detection of G4s in native gels using light-up probes. These molecules become fluorescent after specifically binding to G4s. Several different classes have been discovered, emitting light in various colors, and some possess specificity for certain G4 topologies, which makes them highly versatile tools for G4 visualization. Here, we will explore the general procedure using the light-up probe NMM on RNA G4s and discuss advantages and limitations of this method.
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Affiliation(s)
- Philipp Schult
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Katrin Paeschke
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.
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Fazelifar P, Cucchiarini A, Khoshbin Z, Mergny JL, Kazemi Noureini S. Strong and selective interactions of palmatine with G-rich sequences in TRF2 promoter; experimental and computational studies. J Biomol Struct Dyn 2023:1-15. [PMID: 38100552 DOI: 10.1080/07391102.2023.2292793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 11/25/2023] [Indexed: 12/17/2023]
Abstract
G-rich sequences have the potential to fold into G-quadruplexes (GQs). G-quadruplexes, particularly those positioned in the regulatory regions of proto-oncogenes, have recently garnered attention in anti-cancer drug design. A thermal FRET assay was employed to conduct preliminary screening of various alkaloids, aiming to identify stronger interactions with a specific set of G-rich double-labeled oligonucleotides in both K + and Na + buffers. These oligonucleotides were derived from regions associated with Kit, Myc, Ceb, Bcl2, human telomeres, and potential G-quadruplex forming sequences found in the Nrf2 and Trf2 promoters. Palmatine generally increased the stability of different G-rich sequences into their folded GQ structures, more or less in a concentration dependent manner. The thermal stability and interaction of palmatine was further studied using transition FRET (t-FRET), CD and UV-visible spectroscopy and molecular dynamics simulation methods. Palmatine showed the strongest interaction with T RF2 in both K+ and Na+ buffers even at equimolar concentration ratio. T-FRET studies revealed that palmatine has the potential to disrupt double-strand formation by the T RF2 sequence in the presence of its complementary strand. Palmatine exhibits a stronger interaction with G-rich strand DNA, promoting its folding into G-quadruplex structures. It is noteworthy that palmatine exhibits the strongest interaction with T RF2, which is the shortest sequence among the G-rich oligonucleotides studied, featuring only one nucleotide for two of its loops. Palmatine represents a suitable structure for drug design to develop more specific ligands targeting G-quadruplexes. Whether palmatine can also affect the expression of the T RF2 gene requires further studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pegah Fazelifar
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Zahra Khoshbin
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
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7
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Ji D, Yuan JH, Chen SB, Tan JH, Kwok C. Selective targeting of parallel G-quadruplex structure using L-RNA aptamer. Nucleic Acids Res 2023; 51:11439-11452. [PMID: 37870474 PMCID: PMC10681708 DOI: 10.1093/nar/gkad900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/28/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
G-quadruplexes (G4) are special nucleic acid structures with diverse conformational polymorphisms. Selective targeting of G-quadruplex conformations and regulating their biological functions provide promising therapeutic intervention. Despite the large repertoire of G4-binding tools, only a limited number of them can specifically target a particular G4 conformation. Here, we introduce a novel method, G4-SELEX-Seq and report the development of the first L-RNA aptamer, L-Apt12-6, with high binding selectivity to parallel G4 over other nucleic acid structures. Using parallel dG4 c-kit 1 as an example, we demonstrate the strong binding affinity between L-Apt12-6 and c-kit 1 dG4 in vitro and in cells, and notably report the applications of L-Apt12-6 in controlling DNA replication and gene expression. Our results suggest that L-Apt12-6 is a valuable tool for targeting parallel G-quadruplex conformation and regulating G4-mediated biological processes. Furthermore, G4-SELEX-Seq can be used as a general platform for G4-targeting L-RNA aptamers selection and should be applicable to other nucleic acid structures.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jia-Hao Yuan
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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8
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Singh D, Desai N, Shah V, Datta B. In Silico Identification of Potential Quadruplex Forming Sequences in LncRNAs of Cervical Cancer. Int J Mol Sci 2023; 24:12658. [PMID: 37628839 PMCID: PMC10454738 DOI: 10.3390/ijms241612658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as auxiliary regulators of gene expression influencing tumor microenvironment, metastasis and radio-resistance in cancer. The presence of lncRNA in extracellular fluids makes them promising diagnostic markers. LncRNAs deploy higher-order structures to facilitate a complex range of functions. Among such structures, G-quadruplexes (G4s) can be detected or targeted by small molecular probes to drive theranostic applications. The in vitro identification of G4 formation in lncRNAs can be a tedious and expensive proposition. Bioinformatics-driven strategies can provide comprehensive and economic alternatives in conjunction with suitable experimental validation. We propose a pipeline to identify G4-forming sequences, protein partners and biological functions associated with dysregulated lncRNAs in cervical cancer. We identified 17 lncRNA clusters which possess transcripts that can fold into a G4 structure. We confirmed in vitro G4 formation in the four biologically active isoforms of SNHG20, MEG3, CRNDE and LINP1 by Circular Dichroism spectroscopy and Thioflavin-T-assisted fluorescence spectroscopy and reverse-transcriptase stop assay. Gene expression data demonstrated that these four lncRNAs can be potential prognostic biomarkers of cervical cancer. Two approaches were employed for identifying G4 specific protein partners for these lncRNAs and FMR2 was a potential interacting partner for all four clusters. We report a detailed investigation of G4 formation in lncRNAs that are dysregulated in cervical cancer. LncRNAs MEG3, CRNDE, LINP1 and SNHG20 are shown to influence cervical cancer progression and we report G4 specific protein partners for these lncRNAs. The protein partners and G4s predicted in lncRNAs can be exploited for theranostic objectives.
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Affiliation(s)
- Deepshikha Singh
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India
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9
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Ishiguro A, Ishihama A. ALS-linked TDP-43 mutations interfere with the recruitment of RNA recognition motifs to G-quadruplex RNA. Sci Rep 2023; 13:5982. [PMID: 37046025 PMCID: PMC10097714 DOI: 10.1038/s41598-023-33172-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023] Open
Abstract
TDP-43 is a major pathological protein in sporadic and familial amyotrophic lateral sclerosis (ALS) and mediates mRNA fate. TDP-43 dysfunction leads to causes progressive degeneration of motor neurons, the details of which remain elusive. Elucidation of the molecular mechanisms of RNA binding could enhance our understanding of this devastating disease. We observed the involvement of the glycine-rich (GR) region of TDP-43 in the initial recognition and binding of G-quadruplex (G4)-RNA in conjunction with its RNA recognition motifs (RRM). We performed a molecular dissection of these intramolecular RNA-binding modules in this study. We confirmed that the ALS-linked mutations in the GR region lead to alteration in the G4 structure. In contrast, amino acid substitutions in the GR region alter the protein structure but do not void the interaction with G4-RNA. Based on these observations, we concluded that the structural distortion of G4 caused by these mutations interferes with RRM recruitment and leads to TDP-43 dysfunction. This intramolecular organization between RRM and GR regions modulates the overall G4-binding properties.
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Affiliation(s)
- Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Midori-cho 3-11-15, Koganei, Tokyo, 184-0003, Japan.
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Midori-cho 3-11-15, Koganei, Tokyo, 184-0003, Japan
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Monchaud D. Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology. Acc Chem Res 2023; 56:350-362. [PMID: 36662540 DOI: 10.1021/acs.accounts.2c00757] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Biomimetics is defined as a "practice of making technological design that copies natural processes", with the idea that "nature has already solved the challenges we are trying to solve" (Cambridge Dictionary). The challenge we decided to address several years ago was the selective targeting of G quadruplexes (G4s) by small molecules (G4 ligands). Why? Because G4s, which are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences, are suspected to play key biological roles in human cells and diseases. Selective G4 ligands can thus be used as small-molecule modulators to gain a deep understanding of cell circuitry where G4s are involved, thus complying with the very definition of chemical biology (Stuart Schreiber) applied here to G4 biology. How? Following a biomimetic approach that hinges on the observation that G4s are stable secondary structures owing to the ability of Gs to self-associate to form G quartets, and then of G quartets to self-stack to form the columnar core of G4s. Therefore, using a synthetic G quartet as a G4 ligand represents a unique example of biomimetic recognition of G4s.We formulated this hypothesis more than a decade ago, stepping on years of research on Gs, G4s, and G4 ligands. Our approach led to the design, synthesis, and use of a broad family of synthetic G quartets, also referred to as TASQs for template-assembled synthetic G quartets (John Sherman). This quest led us across various chemical lands (organic and supramolecular chemistry, chemical biology, and genetics), along a route on which every new generation of TASQ was a milestone in the growing portfolio of ever smarter molecular tools to decipher G4 biology. As discussed in this Account, we detail how and why we successively develop the very first prototypes of (i) biomimetic ligands, which interact with G4s according to a bioinspired, like-likes-like interaction between two G quartets, one from the ligand, the other from the G4; (ii) smart ligands, which adopt their active conformation only in the presence of their G4 targets; (iii) twice-as-smart ligands, which act as both smart ligands and smart fluorescent probes, whose fluorescence is triggered (turned on) upon interaction with their G4 targets; and (iv) multivalent ligands, which display additional functionalities enabling the detection, isolation, and identification of G4s both in vitro and in vivo. This quest led us to gather a panel of 14 molecular tools which were used to investigate the biology of G4s at a cellular level, from basic optical imaging to multiomics studies.
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Affiliation(s)
- David Monchaud
- ICMUB, CNRS UMR6302, Université de Bourgogne, 21078 Dijon, France
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11
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Zheng BX, Yu J, Long W, Chan KH, Leung ASL, Wong WL. Structurally diverse G-quadruplexes as the noncanonical nucleic acid drug target for live cell imaging and antibacterial study. Chem Commun (Camb) 2023; 59:1415-1433. [PMID: 36636928 DOI: 10.1039/d2cc05945b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The formation of G-quadruplex structures (G4s) in vitro from guanine (G)-rich nucleic acid sequences of DNA and RNA stabilized with monovalent cations, typically K+ and Na+, under physiological conditions, has been verified experimentally and some of them have high-resolution NMR or X-ray crystal structures; however, the biofunction of these special noncanonical secondary structures of nucleic acids has not been fully understood and their existence in vivo is still controversial at present. It is generally believed that the folding and unfolding of G4s in vivo is a transient process. Accumulating evidence has shown that G4s may play a role in the regulation of certain important cellular functions including telomere maintenance, replication, transcription and translation. Therefore, both DNA and RNA G4s of human cancer hallmark genes are recognized as the potential anticancer drug target for the investigation in cancer biology, chemical biology and drug discovery. The relationship between the sequence, structure and stability of G4s, the interaction of G4s with small molecules, and insights into the rational design of G4-selective binding ligands have been intensively studied over the decade. At present, some G4-ligands have achieved a new milestone and successfully entered the human clinical trials for anticancer therapy. Over the past few decades, numerous efforts have been devoted to anticancer therapy; however, G4s for molecular recognition and live cell imaging and for application as antibacterial agents and antibiofilms against antibiotic resistance have been obviously underexplored. The recent advances in G4-ligands in these areas are thus selected and discussed concentratedly in this article in order to shed light on the emerging role of G4s in chemical biology and therapeutic prospects against bacterial infections. In addition, the recently published molecular scaffolds for designing small ligands selectively targeting G4s in live cell imaging, bacterial biofilm imaging, and antibacterial studies are discussed. Furthermore, a number of underexplored G4-targets from the cytoplasmic membrane-associated DNA, the conserved promoter region of K. pneumoniae genomes, the RNA G4-sites in the transcriptome of E. coli and P. aeruginosa, and the mRNA G4-sites in the sequence for coding the vital bacterial FtsZ protein are highlighted to further explore in G4-drug development against human diseases.
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Affiliation(s)
- Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Jie Yu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Wei Long
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Ka Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China. .,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
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12
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Cueny RR, McMillan SD, Keck JL. G-quadruplexes in bacteria: insights into the regulatory roles and interacting proteins of non-canonical nucleic acid structures. Crit Rev Biochem Mol Biol 2022; 57:539-561. [PMID: 36999585 PMCID: PMC10336854 DOI: 10.1080/10409238.2023.2181310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 04/01/2023]
Abstract
G-quadruplexes (G4s) are highly stable, non-canonical DNA or RNA structures that can form in guanine-rich stretches of nucleic acids. G4-forming sequences have been found in all domains of life, and proteins that bind and/or resolve G4s have been discovered in both bacterial and eukaryotic organisms. G4s regulate a variety of cellular processes through inhibitory or stimulatory roles that depend upon their positions within genomes or transcripts. These include potential roles as impediments to genome replication, transcription, and translation or, in other contexts, as activators of genome stability, transcription, and recombination. This duality suggests that G4 sequences can aid cellular processes but that their presence can also be problematic. Despite their documented importance in bacterial species, G4s remain understudied in bacteria relative to eukaryotes. In this review, we highlight the roles of bacterial G4s by discussing their prevalence in bacterial genomes, the proteins that bind and unwind G4s in bacteria, and the processes regulated by bacterial G4s. We identify limitations in our current understanding of the functions of G4s in bacteria and describe new avenues for studying these remarkable nucleic acid structures.
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Affiliation(s)
- Rachel R. Cueny
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Sarah D. McMillan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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13
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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14
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He Y, Liu M, Teng S, Wojtas L, Gu G, Shi X. Synthesis and Characterization of Fluorescence Active G 4-Quartet and Direct Evaluation of Self-Assembly Impact on Emission. CHINESE CHEM LETT 2022; 33:4203-4207. [PMID: 38107831 PMCID: PMC10723654 DOI: 10.1016/j.cclet.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fluorescence (FL) active 8-aryl guanosine derivatives were prepared and applied for cation mediated self-assembly to form the H-bonded G8-quadruplexes. The p-cyano (p-CN) and 8-anthracene (8-An) substituted guanosines were identified to give the strongest fluorescence with the formation of G8-octamers (G8) both in solution (NMR) and solid state (X-ray). This well-defined G8-octamer system has provided the first direct evidence on the self-assembled G-quadruplex fluorescence emission with aggregation-induced emission (AIE), which could be applied as the foundation for FL molecular probe design toward G-quadruplex recognition.
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Affiliation(s)
- Ying He
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Mengjia Liu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Shun Teng
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Lukasz Wojtas
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Guangxin Gu
- Department of Materials Science, Fudan University, 2005 Songhu Rd., Shanghai, 200438, PR China
| | - Xiaodong Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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15
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Stipaničev N, Raabe K, Rozas I. Aiming to Improve Binding of Porphyrin Diphenyl Guanidinium Conjugates to Guanine-Quadruplexes: When Size Matters. Bioorg Med Chem Lett 2022; 75:128954. [PMID: 36031019 DOI: 10.1016/j.bmcl.2022.128954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Aiming to improve the binding to Guanine quadruplexes of different topologies, docking studies of porphyrin diphenyl guanidine conjugates previously prepared with an O or a S bridge between the diphenyl moiety and a newly design derivative with an SO2 bridge were carried out using different guanine quadruplexes of different topologies (four parallel, one antiparallel and one hybrid). Positive results were obtained from these computational studies drove us to prepare the SO2 bridge conjugate improving the synthetic route previously reported by us. Biophysical experiments such as UV-thermal melting and circular dichroism indicated the lack of binding to the double stranded DNA and poor binding of the new derivative prepared to any of the guanine quadruplexes studied. These results show that the size of this SO2 bridge could be responsible of the poor experimental binding to guanine quadruplexes.
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Affiliation(s)
- Nikolina Stipaničev
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Konstantin Raabe
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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16
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Iida K, Suzuki N, Sasaki A, Ishida S, Arai T. Development of a novel light-up probe for detection of G-quadruplexes in stress granules. Sci Rep 2022; 12:12892. [PMID: 35902691 PMCID: PMC9334577 DOI: 10.1038/s41598-022-17230-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
G-quadruplexes (G4s) regulate various biological processes in cells. However, cellular imaging of dynamically forming G4s in biomolecular condensates using small molecules has been poorly investigated. Herein, we present a fluorescent light-up probe with the ability to selectively stabilize G4s and enhance fluorescence upon G4 binding. The foci of the probe were mainly observed in the nucleoli. These were co-localized with anti-fibrillarin antibodies and anti-G4 antibodies (BG4). Moreover, we tested detection of G4 in stress granules using the developed probe. Stress granules were induced through treatment with not only thapsigargin, but also known G4 ligands (pyridostatin, RHPS4, and BRACO-19). In the stress granules, co-localization between the probe, BG4, and stress granule markers (TIA1 and G3BP1) was detected. We present a practical light-up probe for G4s in stress granules, providing potential targets for G4 ligands.
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Affiliation(s)
- Keisuke Iida
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan.
| | - Natsumi Suzuki
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
| | - Ayano Sasaki
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
| | - Shunsuke Ishida
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
| | - Takayoshi Arai
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
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17
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Lu X, Wu X, Kuang S, Lei C, Nie Z. Visualization of Deep Tissue G-quadruplexes with a Novel Large Stokes-Shifted Red Fluorescent Benzothiazole Derivative. Anal Chem 2022; 94:10283-10290. [PMID: 35776781 DOI: 10.1021/acs.analchem.2c02049] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-quadruplex (G4) is a noncanonical nucleic acid secondary structure that has implications for various physiological and pathological processes and is thus essential to exploring new approaches to G4 detection in live cells. However, the deficiency of molecular imaging tools makes it challenging to visualize the G4 in ex vivo tissue samples. In this study, we established a G4 probe design strategy and presented a red fluorescent benzothiazole derivative, ThT-NA, to detect and image G4 structures in living cells and tissue samples. By enhancing the electron-donating group of thioflavin T (ThT) and optimizing molecular structure, ThT-NA shows excellent photophysical properties, including red emission (610 nm), a large Stokes shift (>100 nm), high sensitivity selectivity toward G4s (1600-fold fluorescence turn-on ratio) and robust two-photon fluorescence emission. Therefore, these features enable ThT-NA to reveal the endogenous RNA G4 distribution in living cells and differentiate the cell cycle by monitoring the changes of RNA G4 folding. Significantly, to the best of our knowledge, ThT-NA is the first benzothiazole-derived G4 probe that has been developed for imaging G4s in ex vivo cancer tissue samples by two-photon microscopy techniques.
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Affiliation(s)
- Xu Lu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Xianhua Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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18
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Zhu J, Bošković F, Keyser UF. Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids. NANO LETTERS 2022; 22:4993-4998. [PMID: 35730196 PMCID: PMC9228402 DOI: 10.1021/acs.nanolett.2c01764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/28/2022] [Indexed: 05/22/2023]
Abstract
Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.
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19
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Umar MI, Chan CY, Kwok CK. Development of RNA G-quadruplex (rG4)-targeting L-RNA aptamers by rG4-SELEX. Nat Protoc 2022; 17:1385-1414. [PMID: 35444329 DOI: 10.1038/s41596-022-00679-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
RNA G-quadruplex (rG4)-SELEX is a method that generates L-RNA aptamers to target an rG4 structure of interest, which can be applied to inhibit G-quadruplex-mediated interactions that have important roles in gene regulation and function. Here we present a Protocol Extension substantially modifying an existing SELEX protocol to describe in detail the procedures involved in performing rG4-SELEX to identify rG4-specific binders that can effectively suppress rG4-peptide and rG4-protein associations. This Protocol Extension improves the speed of aptamer discovery and identification, offering a suite of techniques to characterize the aptamer secondary structure and monitor binding affinity and specificity, and demonstrating the utility of the L-RNA aptamer. The previous protocol mainly describes the identification of RNA aptamers against proteins of interest, whereas in this Protocol Extension we present the development of an unnatural RNA aptamer against an RNA structure of interest, with the potential to be applicable to other nucleic acid motifs or biomolecules. rG4-SELEX starts with a random D-RNA library incubated with the L-rG4 target of interest, followed by binding, washing and elution of the library. Enriched D-aptamer candidates are sequenced and structurally characterized. Then, the L-aptamer is synthesized and used for different applications. rG4-SELEX can be carried out by an experienced molecular biologist with a basic understanding of nucleic acids. The development of rG4-targeting L-RNA aptamers expands the current rG4 toolkit to explore innovative rG4-related applications, and opens new doors to discovering novel rG4 biology in the near future. The duration of each selection cycle as outlined in the protocol is ~2 d.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Chun-Yin Chan
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universtität München, Munich, Germany
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China. .,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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20
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Nucleic Acids as Biotools at the Interface between Chemistry and Nanomedicine in the COVID-19 Era. Int J Mol Sci 2022; 23:ijms23084359. [PMID: 35457177 PMCID: PMC9031702 DOI: 10.3390/ijms23084359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
The recent development of mRNA vaccines against the SARS-CoV-2 infection has turned the spotlight on the potential of nucleic acids as innovative prophylactic agents and as diagnostic and therapeutic tools. Until now, their use has been severely limited by their reduced half-life in the biological environment and the difficulties related to their transport to target cells. These limiting aspects can now be overcome by resorting to chemical modifications in the drug and using appropriate nanocarriers, respectively. Oligonucleotides can interact with complementary sequences of nucleic acid targets, forming stable complexes and determining their loss of function. An alternative strategy uses nucleic acid aptamers that, like the antibodies, bind to specific proteins to modulate their activity. In this review, the authors will examine the recent literature on nucleic acids-based strategies in the COVID-19 era, focusing the attention on their applications for the prophylaxis of COVID-19, but also on antisense- and aptamer-based strategies directed to the diagnosis and therapy of the coronavirus pandemic.
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21
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Georgakopoulos-Soares I, Victorino J, Parada GE, Agarwal V, Zhao J, Wong HY, Umar MI, Elor O, Muhwezi A, An JY, Sanders SJ, Kwok CK, Inoue F, Hemberg M, Ahituv N. High-throughput characterization of the role of non-B DNA motifs on promoter function. CELL GENOMICS 2022; 2:100111. [PMID: 35573091 PMCID: PMC9105345 DOI: 10.1016/j.xgen.2022.100111] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 12/24/2022]
Abstract
lternative DNA conformations, termed non-B DNA structures, can affect transcription, but the underlying mechanisms and their functional impact have not been systematically characterized. Here, we used computational genomic analyses coupled with massively parallel reporter assays (MPRAs) to show that certain non-B DNA structures have a substantial effect on gene expression. Genomic analyses found that non-B DNA structures at promoters harbor an excess of germline variants. Analysis of multiple MPRAs, including a promoter library specifically designed to perturb non-B DNA structures, functionally validated that Z-DNA can significantly affect promoter activity. We also observed that biophysical properties of non-B DNA motifs, such as the length of Z-DNA motifs and the orientation of G-quadruplex structures relative to transcriptional direction, have a significant effect on promoter activity. Combined, their higher mutation rate and functional effect on transcription implicate a subset of non-B DNA motifs as major drivers of human gene-expression-associated phenotypes.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jesus Victorino
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Guillermo E. Parada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | | | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Mubarak Ishaq Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Orry Elor
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Allan Muhwezi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Stephan J. Sanders
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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22
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Trinh KH, Kadam US, Rampogu S, Cho Y, Yang KA, Kang CH, Lee KW, Lee KO, Chung WS, Hong JC. Development of novel fluorescence-based and label-free noncanonical G4-quadruplex-like DNA biosensor for facile, specific, and ultrasensitive detection of fipronil. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:127939. [PMID: 34893377 DOI: 10.1016/j.jhazmat.2021.127939] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Fipronil is a broad-spectrum insecticide widely used in agriculture and residential areas; its indiscriminate use leads to environmental pollution and poses health hazards. Early detection of fipronil is critical to prevent the deleterious effects. However, current insecticide analysis methods such as HPLC, LC/MS, and GC/MS are incompetent; they are costly, immobile, time-consuming, laborious, and need skilled technicians. Hence, a sensitive, specific, and cheap biosensor are essential to containing the contamination. Here, we designed two novel biosensors-the first design relied on fluorescent labeling/quenching, while the second sensor focused on label-free detection using Thioflavin T displacement. Altogether, we identified four candidate aptamers, predicted secondary structures, and performed 3D molecular modeling to predict the binding pocket of fipronil in FiPA6B aptamer. Furthermore, the aptameric sensors showed high sensitivity to fipronil of sub-ppb level LOD, attributed to stringent experimental design. The biosensors displayed high specificity against other phenylpyrazole insecticides and demonstrated robust sensitivity for fipronil in real samples like cabbage and cucumber. Notably, to the best of our knowledge, this is the first demonstration of noncanonical G4-quadruplex-like aptamer binding to fipronil, verified using CD spectroscopy. Such aptasensors possess considerable potential for real-time measurements of hazardous insecticides as point-of-care technology.
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Affiliation(s)
- Kien Hong Trinh
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi City 12400, Vietnam
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Shailima Rampogu
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Yuhan Cho
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Kyung-Ae Yang
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chang Ho Kang
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Keun-Woo Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Woo Sik Chung
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea; Division of Plant Sciences, University of Missouri, Columbia, Missouri, MO 65211, USA.
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23
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Yang SY, Monchaud D, Wong JMY. Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq. Nat Protoc 2022; 17:870-889. [PMID: 35140410 DOI: 10.1038/s41596-021-00671-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/25/2021] [Indexed: 11/09/2022]
Abstract
Guanine-rich RNAs can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), and participate in a wide range of biological processes. Here we describe in detail a G4-RNA-specific precipitation (G4RP) protocol, which enables the transcriptomic profiling of G4-RNAs. The G4RP protocol consists of a chemical cross-linking step, followed by affinity capture with a G4-specific probe, BioTASQ. G4RP can be coupled with sequencing to capture a comprehensive global snapshot of folded G4-RNAs. This method can also be used to profile induced changes (i.e., through G4 ligand treatments) within the G4-RNA transcriptome. The entire protocol can be completed in 1-2 weeks and can be scaled up or down depending on the specific experimental goals. In addition to the protocol details, we also provide here a guide for optimization in different laboratory setups.
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Affiliation(s)
- Sunny Y Yang
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, Dijon, France
| | - Judy M Y Wong
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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24
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I. V. Ramos C, A. S. Almodôvar V, Candeias N, Santos T, Cruz C, Graça P. M. S. Neves M, Tomé AC. Diketopyrrolo[3,4–c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures. Bioorg Chem 2022; 122:105703. [DOI: 10.1016/j.bioorg.2022.105703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022]
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25
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Detecting G4 unwinding. Methods Enzymol 2022; 672:261-281. [DOI: 10.1016/bs.mie.2022.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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27
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Ruggiero E, Zanin I, Terreri M, Richter SN. G-Quadruplex Targeting in the Fight against Viruses: An Update. Int J Mol Sci 2021; 22:ijms222010984. [PMID: 34681641 PMCID: PMC8538215 DOI: 10.3390/ijms222010984] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in anticancer therapy. More recently, exploration of the presence and role of G4s in viral genomes has led to the discovery of G4-regulated key viral pathways. In this context, employment of selective G4 ligands has helped to understand the complexity of G4-mediated mechanisms in the viral life cycle, and highlighted the possibility to target viral G4s as an emerging antiviral approach. Research in this field is growing at a fast pace, providing increasing evidence of the antiviral activity of old and new G4 ligands. This review aims to provide a punctual update on the literature on G4 ligands exploited in virology. Different classes of G4 binders are described, with emphasis on possible antiviral applications in emerging diseases, such as the current COVID-19 pandemic. Strengths and weaknesses of G4 targeting in viruses are discussed.
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28
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Deiana M, Obi I, Andreasson M, Tamilselvi S, Chand K, Chorell E, Sabouri N. A Minimalistic Coumarin Turn-On Probe for Selective Recognition of Parallel G-Quadruplex DNA Structures. ACS Chem Biol 2021; 16:1365-1376. [PMID: 34328300 PMCID: PMC8397291 DOI: 10.1021/acschembio.1c00134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
G-quadruplex (G4)
DNA structures are widespread in the human genome
and are implicated in biologically important processes such as telomere
maintenance, gene regulation, and DNA replication. Guanine-rich sequences
with potential to form G4 structures are prevalent in the promoter
regions of oncogenes, and G4 sites are now considered as attractive
targets for anticancer therapies. However, there are very few reports
of small “druglike” optical G4 reporters that are easily
accessible through one-step synthesis and that are capable of discriminating
between different G4 topologies. Here, we present a small water-soluble
light-up fluorescent probe that features a minimalistic amidinocoumarin-based
molecular scaffold that selectively targets parallel G4 structures
over antiparallel and non-G4 structures. We showed that this biocompatible
ligand is able to selectively stabilize the G4 template resulting
in slower DNA synthesis. By tracking individual DNA molecules, we
demonstrated that the G4-stabilizing ligand perturbs DNA replication
in cancer cells, resulting in decreased cell viability. Moreover,
the fast-cellular entry of the probe enabled detection of nucleolar
G4 structures in living cells. Finally, insights gained from the structure–activity
relationships of the probe suggest the basis for the recognition of
parallel G4s, opening up new avenues for the design of new biocompatible
G4-specific small molecules for G4-driven theranostic applications.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Måns Andreasson
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Shanmugam Tamilselvi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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29
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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30
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Mitteaux J, Lejault P, Wojciechowski F, Joubert A, Boudon J, Desbois N, Gros CP, Hudson RHE, Boulé JB, Granzhan A, Monchaud D. Identifying G-Quadruplex-DNA-Disrupting Small Molecules. J Am Chem Soc 2021; 143:12567-12577. [PMID: 34346684 DOI: 10.1021/jacs.1c04426] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The quest for small molecules that strongly bind to G-quadruplex-DNA (G4), so-called G4 ligands, has invigorated the G4 research field from its very inception. Massive efforts have been invested to discover or rationally design G4 ligands, evaluate their G4-interacting properties in vitro through a series of now widely accepted and routinely implemented assays, and use them as innovative chemical biology tools to interrogate cellular networks that might involve G4s. In sharp contrast, only uncoordinated efforts aimed at developing small molecules that destabilize G4s have been invested to date, even though it is now recognized that such molecular tools would have tremendous application in neurobiology as many genetic and age-related diseases are caused by an overrepresentation of G4s. Herein, we report on our efforts to develop in vitro assays to reliably identify molecules able to destabilize G4s. This workflow comprises the newly designed G4-unfold assay, adapted from the G4-helicase assay implemented with Pif1, as well as a series of biophysical and biochemical techniques classically used to study G4/ligand interactions (CD, UV-vis, PAGE, and FRET-melting), and a qPCR stop assay, adapted from a Taq-based protocol recently used to identify G4s in the genomic DNA of Schizosaccharomyces pombe. This unique, multipronged approach leads to the characterization of a phenylpyrrolocytosine (PhpC)-based G-clamp analog as a prototype of G4-disrupting small molecule whose properties are validated through many different and complementary in vitro evaluations.
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Affiliation(s)
- Jérémie Mitteaux
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Pauline Lejault
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Julien Boudon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, ICB CNRS UMR 6303, UBFC, 21078 Dijon, France
| | - Nicolas Desbois
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Claude P Gros
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196, PSL Research University, 91405 Orsay, France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196, 91405 Orsay, France
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
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31
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Ji D, Lyu K, Zhao H, Kwok CK. Circular L-RNA aptamer promotes target recognition and controls gene activity. Nucleic Acids Res 2021; 49:7280-7291. [PMID: 34233000 PMCID: PMC8287958 DOI: 10.1093/nar/gkab593] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rational design of aptamers to incorporate unnatural nucleotides and special chemical moieties can expand their functional complexity and diversity. Spiegelmer (L-RNA aptamer) is a unique class of aptamer that is composed of unnatural L-RNA nucleotides, and so far there are limited L-RNA aptamer candidates and applications being reported. Moreover, the target binding properties of current L-RNA aptamers require significant improvement. Here, using L-Apt.4-1c as an example, we develop a simple and robust strategy to generate the first circular L-RNA aptamer, cycL-Apt.4-1c, quantitatively, demonstrate substantial enhancement in binding affinity and selectivity toward its target, and notably report novel applications of circular L-RNA aptamer in controlling RNA-protein interaction, and gene activity including telomerase activity and gene expression. Our approach and findings will be applicable to any L-RNA aptamers and open up a new avenue for diverse applications.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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32
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Walia S, Chandrasekaran AR, Chakraborty B, Bhatia D. Aptamer-Programmed DNA Nanodevices for Advanced, Targeted Cancer Theranostics. ACS APPLIED BIO MATERIALS 2021; 4:5392-5404. [PMID: 35006722 DOI: 10.1021/acsabm.1c00413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA has been demonstrated to be a versatile material for construction at the nanoscale. DNA nanodevices are highly programmable and allow functionalization with multiple entities such as imaging modalities (fluorophores), targeting entities (aptamers), drug conjugation (chemical linkers), and triggered release (photoresponsive molecules). These features enhance the use of DNA nanodevices in biological applications, catalyzing the rapid growth of this domain of research. In this review, we focus on recent progress in the development and use of aptamer-functionalized DNA nanodevices as theranostic agents, their characterization, applications as delivery platforms, and advantages. We provide a brief background on the development of aptamers and DNA nanodevices in biomedical applications, and we present specific applications of these entities in cancer diagnosis and therapeutics. We conclude with a perspective on the challenges and possible solutions for the clinical translation of aptamer-functionalized DNA nanodevices in the domain of cancer therapeutics.
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Affiliation(s)
- Shanka Walia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | | | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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33
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Sperti Rota F, Charbonnier T, Lejault P, Zell J, Bernhard C, Valverde IE, Monchaud D. Biomimetic, Smart, and Multivalent Ligands for G-Quadruplex Isolation and Bioorthogonal Imaging. ACS Chem Biol 2021; 16:905-914. [PMID: 33914525 DOI: 10.1021/acschembio.1c00111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
G-quadruplexes (G4s) continue to gather wide attention in the field of chemical biology as their prevalence in the human genome and transcriptome strongly suggests that they play key regulatory roles in cell biology. G4-specific, cell-permeable small molecules (G4-ligands) innovatively permit the interrogation of cellular circuitries in order to assess to what extent G4s influence cell fate and functions. Here, we report on multivalent, biomimetic G4-ligands referred to as TASQs that enable both the isolation and visualization of G4s in human cells. Two biotinylated TASQs, BioTASQ and BioCyTASQ, are indeed efficient molecular tools to isolate G4s from mixtures of nucleic acids through simple affinity capture protocols and to image G4s in cells via a biotin/avidin pretargeted imaging system first applied here to G4s, found to be a reliable alternative to in situ click chemistry.
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Affiliation(s)
| | - Thibaut Charbonnier
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Pauline Lejault
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Joanna Zell
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Claire Bernhard
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Ibai E Valverde
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - David Monchaud
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
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34
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Samani SS, Khojastehnezhad A, Ramezani M, Alibolandi M, Yazdi FT, Mortazavi SA, Khoshbin Z, Abnous K, Taghdisi SM. Ultrasensitive detection of micrococcal nuclease activity and Staphylococcus aureus contamination using optical biosensor technology-A review. Talanta 2021; 226:122168. [DOI: 10.1016/j.talanta.2021.122168] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/02/2023]
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35
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Wickhorst PJ, Ihmels H. Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA. Molecules 2021; 26:2566. [PMID: 33924894 PMCID: PMC8124163 DOI: 10.3390/molecules26092566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/31/2022] Open
Abstract
A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2-7 × 105 M-1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.
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Affiliation(s)
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering (Cµ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany;
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36
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A malachite green light-up aptasensor for the detection of theophylline. Talanta 2021; 232:122417. [PMID: 34074405 DOI: 10.1016/j.talanta.2021.122417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022]
Abstract
Biosensors are of interest for the quantitative detection of small molecules (metabolites, drugs and contaminants for instance). To this end, fluorescence is a widely used technique that is easily associated to aptamers. Light-up aptamers constitute a particular class of oligonucleotides that, specifically induce fluorescence emission when binding to cognate fluorogenic ligands such as malachite green (MG). We engineered a dual aptasensor for theophylline (Th) based on the combination of switching hairpin aptamers specific for MG on the one hand and for Th on the other hand, hence their names: malaswitch (Msw) and theoswitch (Thsw). The two aptaswitches form a loop-loop or kissing Msw-Thsw complex only in the presence of theophylline, allowing binding of MG, subsequently generating a fluorescent signal. The combination of the best Msw and Thsw variants, MswG12 and Thsw19.1, results in a 20-fold fluorescence enhancement of MG at saturating theophylline concentration. This aptasensor discriminates between theophylline and its analogues caffeine and theobromine. Kissing aptaswitches derived from light-up aptamers constitute a novel sensing device.
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37
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Tassinari M, Richter SN, Gandellini P. Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome. Nucleic Acids Res 2021; 49:3617-3633. [PMID: 33721024 PMCID: PMC8053107 DOI: 10.1093/nar/gkab127] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Noncoding RNAs are functional transcripts that are not translated into proteins. They represent the largest portion of the human transcriptome and have been shown to regulate gene expression networks in both physiological and pathological cell conditions. Research in this field has made remarkable progress in the comprehension of how aberrations in noncoding RNA drive relevant disease-associated phenotypes; however, the biological role and mechanism of action of several noncoding RNAs still need full understanding. Besides fulfilling its function through sequence-based mechanisms, RNA can form complex secondary and tertiary structures which allow non-canonical interactions with proteins and/or other nucleic acids. In this context, the presence of G-quadruplexes in microRNAs and long noncoding RNAs is increasingly being reported. This evidence suggests a role for RNA G-quadruplexes in controlling microRNA biogenesis and mediating noncoding RNA interaction with biological partners, thus ultimately regulating gene expression. Here, we review the state of the art of G-quadruplexes in the noncoding transcriptome, with their structural and functional characterization. In light of the existence and further possible development of G-quadruplex binders that modulate G-quadruplex conformation and protein interactions, we also discuss the therapeutic potential of G-quadruplexes as targets to interfere with disease-associated noncoding RNAs.
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Affiliation(s)
- Martina Tassinari
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padova, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, via G. Celoria 26, 20133 Milano, Italy
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38
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Tao Y, Zheng Y, Zhai Q, Wei D. Recent advances in the development of small molecules targeting RNA G-quadruplexes for drug discovery. Bioorg Chem 2021; 110:104804. [PMID: 33740677 DOI: 10.1016/j.bioorg.2021.104804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Extensive evidence indicates that RNA G-quadruplexes have associated with some important cellular events. Investigation of RNA G-quadruplexes is thus vital to revealing their biofunctions. Several small molecules have been developed to target RNA G-quadruplexes to date. Some of the small molecules showed significantly light-up fluorescence signals upon binding to RNA G-quadruplexes, while some of them regulated the biofunctions of RNA G-quadruplexes. In this mini-review, the small molecules divided into four kinds are expounded which focused mainly on their structural features and biological activities. Moreover, we raised the current challenges and promising prospects. This mini-review might contribute to exploiting more sophisticated small molecules targeting RNA G-quadruplexes with high specificity based on the reported chemical structural features.
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Affiliation(s)
- Yanfei Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingge Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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39
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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40
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Influence of core extension and side chain nature in targeting G-quadruplex structures with perylene monoimide derivatives. Bioorg Chem 2021; 108:104660. [PMID: 33550073 DOI: 10.1016/j.bioorg.2021.104660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/31/2022]
Abstract
A structure-activity relationship (SAR) study in terms of G-quadruplex binding ability and antiproliferative activity of six fluorescent perylenemonoimide (PMIs) derivatives is reported. A positive charge seems to be the key to target G4. This study also reveals the importance of the element substitution in the potential biological activity of PMIs, being the polyethylene glycol (PEG) chains in the peri position responsible for their antiproliferative activity. Among them, the cationic PMI6 with two PEG chains is the most promising compound since its fluorescence is enhanced in the presence of G-quadruplex structures. Moreover, PMI6 binds to the human telomeric G-quadruplex hTelo with high affinity and displays a high antiproliferative potential towards HeLa (cervical adenocarcinoma), A549 (lung adenocarcinoma) and A2780 (ovarian adenocarcinoma) cells. Its fate can be followed inside cells thanks to its fluorescent properties: the compound is found to accumulate in the mitochondria.
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41
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Kharel P, Becker G, Tsvetkov V, Ivanov P. Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res 2020; 48:12534-12555. [PMID: 33264409 PMCID: PMC7736831 DOI: 10.1093/nar/gkaa1126] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine-quadruplexes (G4s) are non-canonical four-stranded structures that can be formed in guanine (G) rich nucleic acid sequences. A great number of G-rich sequences capable of forming G4 structures have been described based on in vitro analysis, and evidence supporting their formation in live cells continues to accumulate. While formation of DNA G4s (dG4s) within chromatin in vivo has been supported by different chemical, imaging and genomic approaches, formation of RNA G4s (rG4s) in vivo remains a matter of discussion. Recent data support the dynamic nature of G4 formation in the transcriptome. Such dynamic fluctuation of rG4 folding-unfolding underpins the biological significance of these structures in the regulation of RNA metabolism. Moreover, rG4-mediated functions may ultimately be connected to mechanisms underlying disease pathologies and, potentially, provide novel options for therapeutics. In this framework, we will review the landscape of rG4s within the transcriptome, focus on their potential impact on biological processes, and consider an emerging connection of these functions in human health and disease.
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Affiliation(s)
- Prakash Kharel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gertraud Becker
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Tsvetkov
- Computational Oncology Group, I. M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
- Federal Research and Clinical Center for Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow 117912, Russia
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
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42
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Turcotte MA, Garant JM, Cossette-Roberge H, Perreault JP. Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson's disease. RNA Biol 2020; 18:1339-1353. [PMID: 33305682 PMCID: PMC8354592 DOI: 10.1080/15476286.2020.1847866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous system were initially identified and were found to be significantly enriched. Several G4 sequences found in the 5ʹ untranslated regions (5ʹUTR) of mRNAs associated with Parkinson’s disease were demonstrated to in fact fold in vitro by biochemical assays. Subcloning of the full-length 5ʹUTRs of these candidates upstream of a luciferase reporter system led to the demonstration that the G4s of both Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) significantly repressed the translation of both genes in SH-SY5Y cells. Subsequently, a strategy of using label-free RNA affinity purification assays with either of these two G4 sequences as bait isolated the Guanine Nucleotide-Binding Protein-Like 1 (GNL1). The latter was shown to have a higher affinity for the G4 sequences than for their mutated version. This study sheds light on new RNA G-quadruplexes located in genes dysregulated in Parkinson disease and a new G4-binding protein, GNL1.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Michel Garant
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Hélène Cossette-Roberge
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
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43
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Platform- and label-free detection of lead ions in environmental and laboratory samples using G-quadraplex probes by circular dichroism spectroscopy. Sci Rep 2020; 10:20461. [PMID: 33235290 PMCID: PMC7686487 DOI: 10.1038/s41598-020-77449-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Guanine-rich quadruplex (G-QD) are formed by conversion of nucleotides with specific sequences by stabilization of positively charged K+ or Na+. These G-QD structures differentially absorb two-directional (right- and left-handed) circularly polarized light, which can discriminate the parallel or anti-parallel structures of G-QDs. In this study, G-QDs stabilized by Pb2+ were analyzed by a circular dichroism (CD) spectroscopy to determine Pb2+ concentration in water samples. Thrombin aptamer (TBA), PS2.M, human telomeric DNA (HTG), AGRO 100, and telomeric related sequence (T2) were studied to verify their applicability as probes for platform- and label-free detection of Pb2+ in environmental as well as laboratory samples. Among these nucleotides, TBA and PS2.M exhibited higher binding constants for Pb2+, 1.20-2.04 × 106/M at and 4.58 × 104-1.09 × 105/M at 100 micromolar and 100 mM K+ concentration, respectively. They also exhibited excellent selectivity for Pb2+ than for Al3+, Cu2+, Ni2+, Fe3+, Co2+, and Cr2+. When Pb2+ was spiked into an effluent sample from a wastewater treatment plant (WWTP), its existence was detected by CD spectroscopy following a simple addition of TBA or PS2.M. By the addition of TBA and PS2.M, the Pb2+ signals were observed in effluent samples over 0.5 micromolar (100 ppb) concentration. Furthermore, PS2.M caused a Pb2+-specific absorption band in the effluent sample without spiking of Pb2+, and could be induced to G-QD structure by the background Pb2+ concentration in the effluent, 0.159 micromolar concentration (3.30 ppb). Taken together, we propose that TBA and PS2.M are applicable as platform- and label-free detection probes for monitoring Pb2+ in environmental samples such as discharged effluent from local WWTPs, using CD spectroscopy.
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44
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Shahsavar K, Shokri E, Hosseini M. A fluorescence-readout method for miRNA-155 detection with double-hairpin molecular beacon based on quadruplex DNA structure. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105277] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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45
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Imperatore C, Varriale A, Rivieccio E, Pennacchio A, Staiano M, D’Auria S, Casertano M, Altucci C, Valadan M, Singh M, Menna M, Varra M. Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides. Int J Mol Sci 2020; 21:ijms21197103. [PMID: 32993097 PMCID: PMC7582650 DOI: 10.3390/ijms21197103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
The synthesis of two 5′-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5′-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5′-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.
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Affiliation(s)
- Concetta Imperatore
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Antonio Varriale
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Elisa Rivieccio
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Angela Pennacchio
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Maria Staiano
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Sabato D’Auria
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Marcello Casertano
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Carlo Altucci
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Mohammadhassan Valadan
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Manjot Singh
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Marialuisa Menna
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Michela Varra
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
- Correspondence: ; Tel.: +39-081-678540
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Deiana M, Chand K, Jamroskovic J, Das RN, Obi I, Chorell E, Sabouri N. A site-specific self-assembled light-up rotor probe for selective recognition and stabilization of c-MYC G-quadruplex DNA. NANOSCALE 2020; 12:12950-12957. [PMID: 32525170 DOI: 10.1039/d0nr03404e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Direct and unambiguous evidence of the formation of G-quadruplexes (G4s) in human cells have shown their implication in several key biological events and has emphasized their role as important targets for small-molecule cancer therapeutics. Here, we report on the first example of a self-assembled molecular-rotor G4-binder able to discriminate between an extensive panel of G4 and non-G4 structures and to selectively light-up (up to 64-fold), bind (nanomolar range), and stabilize the c-MYC promoter G4 DNA. In particular, association with the c-MYC G4 triggers the disassembly of its supramolecular state (disaggregation-induced emission, DIE) and induces geometrical restrictions (motion-induced change in emission, MICE) leading to a significant enhancement of its emission yield. Moreover, this optical reporter is able to selectively stabilize the c-MYC G4 and inhibit DNA synthesis. Finally, by using confocal laser-scanning microscopy (CLSM) we show the ability of this compound to localize primarily in the subnuclear G4-rich compartments of cancer cells. This work provides a benchmark for the future design and development of a new generation of smart sequence-selective supramolecular G4-binders that combine outstanding sensing and stability properties, to be utilized in anti-cancer therapy.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | | | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
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47
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Phthalocyanines for G-quadruplex aptamers binding. Bioorg Chem 2020; 100:103920. [PMID: 32413624 DOI: 10.1016/j.bioorg.2020.103920] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
The G-quadruplex (G4)-forming sequence within the AS1411 derivatives with alternative nucleobases and backbones can improve the chemical and biological properties of AS1411. Zn(II) phthalocyanine (ZnPc) derivatives have potential as high-affinity G4 ligands because they have similar size and shape to the G-quartets. The interactions of four Zn(II) phthalocyanines with the G4 AS1411 aptamer and its derivatives were determined by biophysical techniques, molecular docking and gel electrophoresis. Cell viability assay was carried out to evaluate the antiproliferative effects of Zn(II) phthalocyanines and complexes. CD experiments showed structural changes after addition of ZnPc 4, consistent with multiple binding modes and conformations shown by NMR and gel electrophoresis. CD melting confirmed that ZnPc 2 and ZnPc 4, both containing eight positive charges, are able to stabilize the AT11 G4 structure (ΔTm > 30 °C and 18.5 °C, respectively). Molecular docking studies of ZnPc 3 and ZnPc 4 suggested a preferential binding to the 3'- and 5'-end, respectively, of the AT11 G4. ZnPc 3 and its AT11 and AT11-L0 complexes revealed pronounced cytotoxic effect against cervical cancer cells and no cytotoxicity to normal human cells. Zn(II) phthalocyanines provide the basis for the development of effective therapeutic agents as G4 ligands.
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48
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Hong CY, Zhang XX, Dai CY, Wu CY, Huang ZY. Highly sensitive detection of multiple antibiotics based on DNA tetrahedron nanostructure-functionalized magnetic beads. Anal Chim Acta 2020; 1120:50-58. [PMID: 32475391 DOI: 10.1016/j.aca.2020.04.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 01/03/2023]
Abstract
Functional DNAs-functionalized magnetic beads (MBs) offer great potential in bioanalysis field because of their target recognition and magnetic separation functions. However, the recognition capability and hybridization affinity of DNA probes often suffer from limited available space, poor probe conformation and non-selective adsorption. To overcome these limitations, we herein used aptamer-pendant DNA tetrahedron nanostructure-functionalized MBs (TETapt-tet MBs) to develop a target-response fluorescence method with tetracycline (TET) as a model. In the absence of TET, 6-carboxy-X-rhodamine-labeled complementary DNAs (ROX-cDNAs) were assembled on the surface of MBs. Upon the addition of target TET, the ROX-cDNAs were separated and released from the MBs to generate fluorescence signal. The limit of detection and limit of quantification for TET were found to be 6 pg mL-1 and 20 pg mL-1, respectively. Compared with ssDNA-functionalized MBs surface, the designed DNA tetrahedron nanostructure-based surface could decrease the hybridization time and reduce false positives, ensuring the accuracy of TET detection in complex samples. The presented method was successfully employed for TET detection in honey samples. Moreover, this functionalization strategy could be extended to detect multiple antibiotics by simply substituting different aptamer sequences. Therefore, the proposed method has great potential in the field of food safety and public health.
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Affiliation(s)
- Cheng-Yi Hong
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Xiao-Xia Zhang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chen-Ying Dai
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chen-Yue Wu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zhi-Yong Huang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, 361021, China.
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49
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Chan C, Kwok CK. Specific Binding of a
d
‐RNA G‐Quadruplex Structure with an
l
‐RNA Aptamer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Chun‐Yin Chan
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
| | - Chun Kit Kwok
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
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50
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Chan CY, Kwok CK. Specific Binding of a d-RNA G-Quadruplex Structure with an l-RNA Aptamer. Angew Chem Int Ed Engl 2020; 59:5293-5297. [PMID: 31975549 DOI: 10.1002/anie.201914955] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/06/2020] [Indexed: 01/24/2023]
Abstract
G-quadruplex (G4) structures are of general importance in chemistry and biology, such as in biosensing, gene regulation, and cancers. Although a large repertoire of G4-binding tools has been developed, no aptamer has been developed to interact with G4. Moreover, the G4 selectivity of current toolkits is very limited. Herein, we report the first l-RNA aptamer that targets a d-RNA G-quadruplex (rG4). Using TERRA rG4 as an example, our results reveal that this l-RNA aptamer, Ap3-7, folds into a unique secondary structure, exhibits high G4 selectivity and effectively interferes with TERRA-rG4-RHAU53 binding. Our approach and findings open a new door in further developing G4-specific tools for diverse applications.
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Affiliation(s)
- Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
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