1
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Andregic N, Weaver C, Basu S. The binding of a c-MYC promoter G-quadruplex to neurotransmitters: An analysis of G-quadruplex stabilization using DNA melting, fluorescence spectroscopy, surface-enhanced Raman scattering and molecular docking. Biochim Biophys Acta Gen Subj 2023; 1867:130473. [PMID: 37778448 DOI: 10.1016/j.bbagen.2023.130473] [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: 07/14/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The interactions of several neurotransmitter and neural hormone molecules with the c-MYC G-quadruplex DNA sequence were analyzed using a combination of spectroscopic and computational techniques. The interactions between indole, catecholamine, and amino acid neurotransmitters and DNA sequences could potentially add to the understanding of the role of G-quadruplex structures play in various diseases. Also, the interaction of the DNA sequence derived from the nuclear hypersensitivity element (NHE) III1 region of c-MYC oncogene (Pu22), 5'-TGAGGGTGGGTAGGGTGGGTAA-3', has added significance in that these molecules may promote or inhibit the formation of G-quadruplex DNA which could lead to the development of promising drugs for anticancer therapy. The results showed that these molecules did not disrupt G-quadruplex formation even in the absence of quadruplex-stabilizing cations. There was also evidence of concentration-dependent binding and high binding affinities based on the Stern-Volmer model, and thermodynamically favorable interactions in the form of hydrogen-bonding and interactions involving the π system of the aromatic neurotransmitters.
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Affiliation(s)
- Nicole Andregic
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Caitlin Weaver
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Swarna Basu
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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2
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Guan Z, Sun Y, Ma CB, Lee JJ, Zhang S, Zhang X, Guo Z, Du Y. Dual targets-induced specific hemin/G-quadruplex assemblies for label-free electrochemical detection capable of distinguishing Salmonella and its common serotype in food samples. Biosens Bioelectron 2023; 236:115438. [PMID: 37263053 DOI: 10.1016/j.bios.2023.115438] [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: 03/24/2023] [Revised: 05/12/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
Efficient detection of pathogenic bacteria is paramount for ensuring food safety and safeguarding public health. Herein, we developed a label-free and signal-on dual-target recognition electrochemical DNA sensing platform based on the conformational formation of split G-quadruplex. This platform focused on achieving sensitive and low-cost detection of Salmonella and its most human-infecting S. typhimurium serotype. In simple terms, the dual-target recognition probe (DTR-6P) was ingeniously designed for the loop sequence on the loop-mediated isothermal amplification (LAMP) amplicons. It could recognize two different genes and release their corresponding G-rich sequences. The exfoliated G-rich sequences could be captured by the capture probes on the electrode, and then the bimolecular G-quadruplex or the tetramolecular G-quadruplex would be formed to capture hemin, thereby enabling dual-signal reporting. The minimum detection amount of target genes can be as low as 2 copies/μL. Encouragingly, the real food samples contaminated by Salmonella and the S. typhimurium serotype can be readily identified. The sensing platform with ingenious design paves a new way for label-free, multi-target simultaneous detection, whose advantage of rapidity, sensitivity, cost-effectiveness, and specificity also lay a solid foundation for practical applications.
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Affiliation(s)
- Zhaowei Guan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin, 133002, China; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Food Science and Engineering, Yanbian University, YanJi, Jilin, 133002, China
| | - Yi Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Chong-Bo Ma
- Key Laboratory of Polyoxometalate Science of Ministry of Education, National & Local United Engineering Laboratory for Power Batteries, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, Changchun, Jilin, 130024, China
| | - Jung Joon Lee
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin, 133002, China
| | - Sicai Zhang
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin, 133002, China; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiaojun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Zhijun Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin, 133002, China; Department of Food Science and Engineering, Yanbian University, YanJi, Jilin, 133002, China.
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China; Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China.
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3
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Endoh T, Takahashi S, Sugimoto N. Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase. Chem Commun (Camb) 2023; 59:872-875. [PMID: 36594508 DOI: 10.1039/d2cc05858h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan
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4
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Brush GS. Anomalies in dye-terminator DNA sequencing caused by a natural G-quadruplex. PLoS One 2022; 17:e0279423. [PMID: 36574393 PMCID: PMC9794070 DOI: 10.1371/journal.pone.0279423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/24/2022] [Indexed: 12/29/2022] Open
Abstract
A G-rich DNA sequence from yeast that can form a non-canonical G-quadruplex structure was cloned into a plasmid vector and subjected to Sanger sequencing using dye-labeled dideoxynucleotides. Two different effects were observed. In one, presence of the G4 sequence on the template strand led to incorrect incorporation of an A residue at an internal position in the G4 sequence. In the other, the nascent strand caused attenuation of the readout coincident with synthesis of the G-rich DNA. The two effects are novel examples of disruption in DNA synthesis caused by a G4 sequence. These results provide a new example of a DNA structure that could influence genomic stability in human cells.
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Affiliation(s)
- George S. Brush
- Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine,Detroit, MI, United States of America
- * E-mail:
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5
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Criscuolo A, Napolitano E, Riccardi C, Musumeci D, Platella C, Montesarchio D. Insights into the Small Molecule Targeting of Biologically Relevant G-Quadruplexes: An Overview of NMR and Crystal Structures. Pharmaceutics 2022; 14:pharmaceutics14112361. [PMID: 36365179 PMCID: PMC9696056 DOI: 10.3390/pharmaceutics14112361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
G-quadruplexes turned out to be important targets for the development of novel targeted anticancer/antiviral therapies. More than 3000 G-quadruplex small-molecule ligands have been described, with most of them exerting anticancer/antiviral activity by inducing telomeric damage and/or altering oncogene or viral gene expression in cancer cells and viruses, respectively. For some ligands, in-depth NMR and/or crystallographic studies were performed, providing detailed knowledge on their interactions with diverse G-quadruplex targets. Here, the PDB-deposited NMR and crystal structures of the complexes between telomeric, oncogenic or viral G-quadruplexes and small-molecule ligands, of both organic and metal-organic nature, have been summarized and described based on the G-quadruplex target, from telomeric DNA and RNA G-quadruplexes to DNA oncogenic G-quadruplexes, and finally to RNA viral G-quadruplexes. An overview of the structural details of these complexes is here provided to guide the design of novel ligands targeting more efficiently and selectively cancer- and virus-related G-quadruplex structures.
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Affiliation(s)
- Andrea Criscuolo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
- Institute of Biostructures and Bioimages, CNR, 80134 Naples, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
- Correspondence:
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
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6
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Luo Y, Verga D, Mergny JL. Iso-FRET: an isothermal competition assay to analyze quadruplex formation in vitro. Nucleic Acids Res 2022; 50:e93. [PMID: 35670668 PMCID: PMC9458428 DOI: 10.1093/nar/gkac465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/26/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
Algorithms have been widely used to predict G-quadruplexes (G4s)-prone sequences. However, an experimental validation of these predictions is generally required. We previously reported a high-throughput technique to evidence G4 formation in vitro called FRET-MC. This method, while convenient and reproducible, has one known weakness: its inability to pin point G4 motifs of low thermal stability. As such quadruplexes may still be biologically relevant if formed at physiological temperature, we wanted to develop an independent assay to overcome this limitation. To this aim, we introduced an isothermal version of the competition assay, called iso-FRET, based on a duplex-quadruplex competition and a well-characterized bis-quinolinium G4 ligand, PhenDC3. G4-forming competitors act as decoys for PhenDC3, lowering its ability to stabilize the G4-forming motif reporter oligonucleotide conjugated to a fluorescence quencher (37Q). The decrease in available G4 ligand concentration restores the ability of 37Q to hybridize to its FAM-labeled short complementary C-rich strand (F22), leading to a decrease in fluorescence signal. In contrast, when no G4-forming competitor is present, PhenDC3 remains available to stabilize the 37Q quadruplex, preventing the formation of the F22 + 37Q complex. Iso-FRET was first applied to a reference panel of 70 sequences, and then used to investigate 23 different viral sequences.
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Affiliation(s)
- Yu Luo
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France
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7
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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: 0] [Impact Index Per Article: 0] [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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8
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Holoubek J, Bednářová K, Haviernik J, Huvarová I, Dvořáková Z, Černý J, Outlá M, Salát J, Konkol'ová E, Boura E, Růžek D, Vorlíčková M, Eyer L, Renčiuk D. Guanine quadruplexes in the RNA genome of the tick-borne encephalitis virus: their role as a new antiviral target and in virus biology. Nucleic Acids Res 2022; 50:4574-4600. [PMID: 35420134 PMCID: PMC9071444 DOI: 10.1093/nar/gkac225] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022] Open
Abstract
We have identified seven putative guanine quadruplexes (G4) in the RNA genome of tick-borne encephalitis virus (TBEV), a flavivirus causing thousands of human infections and numerous deaths every year. The formation of G4s was confirmed by biophysical methods on synthetic oligonucleotides derived from the predicted TBEV sequences. TBEV-5, located at the NS4b/NS5 boundary and conserved among all known flaviviruses, was tested along with its mutated variants for interactions with a panel of known G4 ligands, for the ability to affect RNA synthesis by the flaviviral RNA-dependent RNA polymerase (RdRp) and for effects on TBEV replication fitness in cells. G4-stabilizing TBEV-5 mutations strongly inhibited RdRp RNA synthesis and exhibited substantially reduced replication fitness, different plaque morphology and increased sensitivity to G4-binding ligands in cell-based systems. In contrast, strongly destabilizing TBEV-5 G4 mutations caused rapid reversion to the wild-type genotype. Our results suggest that there is a threshold of stability for G4 sequences in the TBEV genome, with any deviation resulting in either dramatic changes in viral phenotype or a rapid return to this optimal level of G4 stability. The data indicate that G4s are critical elements for efficient TBEV replication and are suitable targets to tackle TBEV infection.
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Affiliation(s)
- Jiří Holoubek
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Jan Haviernik
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Ivana Huvarová
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic
| | - Zuzana Dvořáková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Jiří Černý
- Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, CZ-16500 Prague, Czech Republic
| | - Martina Outlá
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Jiří Salát
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Eva Konkol'ová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy ofSciences, CZ-16000 Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy ofSciences, CZ-16000 Prague, Czech Republic
| | - Daniel Růžek
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Michaela Vorlíčková
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
| | - Luděk Eyer
- Veterinary Research Institute, Emerging Viral Diseases, Brno CZ-62100, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic
| | - Daniel Renčiuk
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61200, Czech Republic
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9
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Jawarkar RD, Bakal RL, Khatale PN, Lewaa I, Jain CM, Manwar JV, Jaiswal MS. QSAR, pharmacophore modeling and molecular docking studies to identify structural alerts for some nitrogen heterocycles as dual inhibitor of telomerase reverse transcriptase and human telomeric G-quadruplex DNA. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA are amongst the favorable target for researchers to discover novel and more effective anticancer agents. To understand and elucidate structure activity relationship and mechanism of inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA, a QSAR modeling and molecular docking were conducted.
Results
Two robust QSAR model were obtained which consist of full set QSAR model (R2: 0.8174, CCCtr: 0.8995, Q2loo: 0.7881, Q2LMO: 0.7814) and divided set QSAR model (R2: 0.8217, CCCtr: 0.9021, Q2loo: 0.7886, Q2LMO: 0.7783, Q2-F1: 0.7078, Q2-F2: 0.6865, Q2-F3: 0.7346) for envisaging the inhibitory activity of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The analysis reveals that carbon atom exactly at 3 bonds from aromatic carbon atom, nitrogen atom exactly at six bonds from planer nitrogen atom, aromatic carbon atom within 2 A0 from the center of mass of molecule and occurrence of element hydrogen within 2 A0 from donar atom are the key pharmacophoric features important for dual inhibition of TERT and human telomeric G-quadruplex DNA. To validate this analysis, pharmacophore modeling and the molecular docking is performed. Molecular docking analysis support QSAR analysis and revealed that, dual inhibition of TERT and human telomeric DNA is mainly contributed from hydrophobic and hydrogen bonding interactions.
Conclusion
The findings of molecular docking, pharmacophore modelling, and QSAR are all consistent and in strong agreement. The validated QSAR analyses can detect structural alerts, pharmacophore modelling can classify a molecule's consensus pharmacophore involving hydrophobic and acceptor regions, whereas docking analysis can reveal the mechanism of dual inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The combination of QSAR, pharmacophore modeling and molecular docking may be useful for the future drug design of dual inhibitors to combat the devastating issue of resistance.
Graphical abstract
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10
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Cao Y, Li W, Pei R. Manipulating the Assembly of DNA Nanostructures and Their Enzymatic Properties by Incorporating a 5'-5' Polarity of Inversion Site in the G-Tract. ACS Macro Lett 2021; 10:1359-1364. [PMID: 35549016 DOI: 10.1021/acsmacrolett.1c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Supramolecular DNA complexes consisting of both DNA duplexes and tetrameric G-quadruplexes are fabricated successfully by utilizing a single short DNA strand that contains one 5'-5' polarity of inversion site in the middle of G-tract. The resulting DNA supramolecules exhibit significantly high peroxidase activities after interaction with hemin due to the presence of various G-quadruplex-duplex (G4-duplex) interfaces. Significantly, we find that the addition of a C-rich fragment to the designed sequence not only allows the self-assembly of two-dimensional porous DNA nanostructures via the formation of dimeric i-motif structures but also could act as a control element to facilitate the generation of pH-sensitive G4-based DNAzymes. The enhanced catalytic activity obtained from specific sequence modifications as well as the controllable feature of these DNA nanostructures can significantly benefit further applications of DNA functional materials in complex biological systems.
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Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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11
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Xia X, Ma B, Zhang T, Lu Y, Khan MR, Hu Y, Lei C, Deng S, He Q, He G, Zhang K, Deng R. G-Quadruplex-Probing CRISPR-Cas12 Assay for Label-Free Analysis of Foodborne Pathogens and Their Colonization In Vivo. ACS Sens 2021; 6:3295-3302. [PMID: 34516103 DOI: 10.1021/acssensors.1c01061] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Foodborne pathogen infection is a key issue of food safety. Herein, we developed a label-free assay for Salmonella enterica (S. enterica) detection based on the G-quadruplex-probing CRISPR-Cas12 system (termed G-CRISPR-Cas), allowing highly sensitive detection of S. enterica and investigation of their colonization in chickens. The introduction of the G-quadruplex probe serving as the substrate of Cas 12a realized a label-free analysis for foodborne pathogens. Due to the amplification process induced by loop-mediated isothermal amplification (LAMP), G-CRISPR-Cas assay can detect S. enterica as low as 20 CFU. Specificity for pathogenic gene detection was guaranteed by the dual recognition process via LAMP primers and Cas 12a-guided RNA binding. The G-CRISPR-Cas assay was applied to explore S. enterica colonization in the intestinal tract and organs of chickens and showed the risk of S. enterica infection outside of the intestinal tract. The G-CRISPR-Cas assay is promising for on-site diagnosis of the infection or contamination of foodborne pathogens outside the laboratories, such as abattoirs and markets.
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Affiliation(s)
- Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Boheng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yunhao Lu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yun Hu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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12
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Abstract
Ribonucleases are useful as biomarkers and can be the source of contamination in laboratory samples, making ribonuclease detection assays important in life sciences research. With recent developments in DNA-based biosensing, several new techniques are being developed to detect ribonucleases. This review discusses some of these methods, specifically those that utilize G-quadruplex DNA structures, DNA-nanoparticle conjugates and DNA nanostructures, and the advantages and challenges associated with them.
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13
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Xu M, Peng Y, Liu H, Tian X, Yang H, Zhou Y. A label-free ratiometric method to detect Hg 2+ based on structural change of DNA. LUMINESCENCE 2021; 36:1985-1990. [PMID: 34435442 DOI: 10.1002/bio.4134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022]
Abstract
In this work, a simple ratiometric method has been designed to detect Hg2+ based on the structural change between double-stranded DNA (dsDNA) and its G-quadruplex structure. When Hg2+ was added, the designed G-quadruplex structure could change into the corresponding dsDNA by forming the T-Hg2+ -T mismatch. This kind of variation resulted in a decrease in the fluorescence of the G-quadruplex/N-methyl mesoporphyrin IX (NMM) complex and an increase in the fluorescence from the dsDNA/SYBR Green I (SG I) pair. The secondary excitation wavelength of SG I was used to excite NMM and SG I simultaneously. The titration experiment indicated that the new method had a linear response within 0.7-2.5 μM Hg2+ with a limit of detection of 9.3 nM. Because using the T-Hg2+ -T mismatch to recognize Hg2+ was very specific, the selectivity of the new method was also satisfactory. The recoveries ranged from 92.8% to 110.2% suggested that this new method could achieve a potential application for Hg2+ detection in real environmental samples.
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Affiliation(s)
- Mingming Xu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Yu Peng
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Huan Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Xinyu Tian
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Hualin Yang
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, China
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14
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Hu W, Wang Y, Qian M, Wang L, Dong Y. A Label-free "Lock-key" Fluorescence Aptasensing Based on Triplex-helix DNA and G-quadruplex for CA15-3 Detection. ANAL SCI 2021; 37:905-909. [PMID: 33162412 DOI: 10.2116/analsci.20p332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Herein, we designed a label-free fluorescent aptasensor based on triple-helix DNA and G-quadruplex for carbohydrate antigen (CA15-3) detection. The triplex-helix structure can be formed with inserted G-rich DNA (IG) and aptamer DNA (Apt), which like a "lock" to lock the G-rich sequences. The CA15-3 was the "key", which specifically combined with aptamer sequences of Apt, resulting in liberating IG from the triplex-helix "lock". Then, the G-rich sequences of IG were formed into G-quadruplex and specifically interacted with N-methylmesoporphyrin IX (NMM), which greatly enhanced the fluorescence of the solution. However, when the "key" did not exist, the "lock" was fastened and fluorescence intensity did not change. With this proposed method, the concentration of CA15-3 can be effectively detected from 0.01 to 5 U mL-1 with a detection limit (LOD) of 0.01 U mL-1. Furthermore, this proposed biosensor can be applied to spiked human serum with great precision and reproducibility.
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Affiliation(s)
- Wenxiao Hu
- School of Life Sciences, Shaanxi Normal University
| | - Yue Wang
- College of Computer Sciences, Shaanxi Normal University
| | - Mengyao Qian
- College of Computer Sciences, Shaanxi Normal University
| | - Luhui Wang
- School of Life Sciences, Shaanxi Normal University
| | - Yafei Dong
- School of Life Sciences, Shaanxi Normal University.,Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China
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15
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Huang C, Xu X, Jiang D, Jiang W. Binding mediated MNAzyme signal amplification strategy for enzyme-free and label-free detection of DNA-binding proteins. Anal Chim Acta 2021; 1166:338560. [PMID: 34022996 DOI: 10.1016/j.aca.2021.338560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
A novel MNAzyme signal amplification strategy was developed for enzyme-free and label-free detection of DNA-binding proteins. This strategy relied on the binding-mediated MNAzyme cleavage and G-quadruplex-based light-up fluorescence switch. Three DNA sequences were designed to construct the MNAzyme in which DNA1 (including half binding site of the target protein and a toehold sequence) and DNA2 (including another half binding site of the target protein and one MNAzyme partzyme) firstly hybridized. The target protein recognized the binding sites on DNA1-DNA2 hybrid to form a stable protein-DNA1-DNA2 conjugates. Then, the MNAzyme was assembled with the presence of DNA3 which contained another MNAzyme partzyme and the complementary sequence of DNA1. The active MNAzyme cleaved DNA4 to release the G-quadruplex that was locked in the stem of DNA4. Finally, N-methyl mesoporphyrin IX (NMM) was inserted into the released G-quadruplex structure and the fluorescence signal was turned on. Taking nuclear factor-κB p50 (NF-κB p50) as the model, the limit of detection was low to 0.14 nM. Furthermore, the sequence-specific recognition of NF-κB p50 with DNA displayed excellent selectivity and specificity. The results in present work showed that this strategy will be a promising tool for DNA-binding proteins analysis in biomedical exploration and clinical diagnosis.
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Affiliation(s)
- Chao Huang
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Xiaowen Xu
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Dafeng Jiang
- Department of Physical and Chemical Testing, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, 250014, Jinan, PR China.
| | - Wei Jiang
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China; School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
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16
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Yu C, Wang Y, Wu R, Zhu Z, Li B. Study on the Functionalization and Signaling Efficiency of the Hybridization Chain Reaction Using Traditional and Single Molecular Characterizations. ACS APPLIED BIO MATERIALS 2021; 4:3649-3657. [PMID: 35014450 DOI: 10.1021/acsabm.1c00136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As an important enzyme-free amplifier, the hybridization chain reaction (HCR) uses an ssDNA to trigger cycled displacement interactions between substrate hairpins and finally form elongated dsDNA concatamer mixtures. In many cases, to provide a signal probe or advanced function, additional oligonucleotides (named hairpin tails) have to be extended upon classic HCR hairpin substrates, but by doing so the HCR assembly efficiency and signal-to-noise ratio (SNR) may get seriously reduced. In this Article, a rational and general model that may guide the study on HCR functionalization and signaling efficiency is provided. We rationally design a four-hairpin model HCR system (4H-HCR) in which one or more hairpin substrates are appended with additional tails as a signaling probe. After HCR assembly, two adjacent tails are supposedly integrating into a full G-quadruplex structure to provide the evidence or signal for the assembly. A systematic study has been applied to reveal the relationship between the "tail-design" with assembly efficiency and SNR. A clear design rule-set guiding the optimized assembly and signal has been provided for traditional electrophoresis and G-quadruplex-enhanced fluorescence signal. Importantly, solid-state nanopore single molecular detection has been innovatively introduced and recommended as an "antirisk" and "mutual benefit" readout to traditional G-quadruplex signaling. Nanopore detection can provide a clear signal distinguished before and after the HCR reaction, especially when the traditional G-quadruplex-enhanced signal only provides low SNR. The G-quadruplex, in turn, may enhance the nanopore signal amplitude via increasing the diameter of the HCR products.
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Affiliation(s)
- Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Zhentong Zhu
- College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu 730070, People's Republic of China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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17
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New insight into G-quadruplexes; diagnosis application in cancer. Anal Biochem 2021; 620:114149. [PMID: 33636157 DOI: 10.1016/j.ab.2021.114149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Biochemical properties and flexibility of nitrogenous bases allow DNA to fold into higher-order structures. Among different DNA secondary structure, G-quadruplexes (tetrapelexes-G4) - which are formed in guanine rich sequences - have gained more attention because of their biological significance, therapeutic intervention, and application in molecular device and biosensor. G4-quadruplex studies categorize into three main fields, in vivo, in vitro, and in silico. The in vitro field includes G4 synthetic oligonucleotides. This review focuses on the G-quadruplex synthetic aptamers structure features and considers the applicability of G4-aptamers for cancer biomarkers detection. Various biosensing methods will be reviewed based on G-quadruplex aptamers for cancer detection.
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18
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Francis S, Rajith L. Selective Fluorescent Sensing of Adenine Via the Emissive Enhancement of a Simple Cobalt Porphyrin. J Fluoresc 2021; 31:577-586. [PMID: 33481138 DOI: 10.1007/s10895-021-02685-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/11/2021] [Indexed: 11/24/2022]
Abstract
Porphyrins absorb strongly in the visible region and are also excellent fluorophores that emit in the visible region that make them excellent candidates for fluorescence sensing and in vivo imaging. This work describes the fluorescence determination of adenine using cobalt complex of a simple porphyrin. Tetraphenylporphyrin (TPP) and tetraphenylpophyrinatocobalt(II) (CoTPP) were synthesized and characterised. TPP on metallation with cobalt resulted in the red shift of fluorescence emission in the region 652 nm and 716 nm and showed an enhancement in the emission peaks with the addition of the nucleobase, adenine. CoTPP is found to be an efficient fluorescent sensor for adenine in DMF solvent. The fluorescence enhancement is due to the formation of the ground state complex formation between adenine and CoTPP, which is supported by experimental evidences from UV- visible spectra, time resolved fluorescence life time measurements etc. The detection limit of adenine was found to be 4.2 μM using the CoTPP fluorescent probe. The proposed sensor is found to be highly selective for adenine in presence of other nitrogen bases like guanine, cytosine, uracil, thymine, alanine, histidine etc. in 1:1 concentration.
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Affiliation(s)
- Shijo Francis
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala, 682022, India
| | - Leena Rajith
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala, 682022, India.
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19
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20
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Wu Y, Yue Y, Deng S, He G, Gao H, Zhou M, Zhong K, Deng R. Ratiometric-enhanced G-Quadruplex Probes for Amplified and Mix-to-Read Detection of Mercury Pollution in Aquatic Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12124-12131. [PMID: 33058672 DOI: 10.1021/acs.jafc.0c05658] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mercury, as a global toxic pollutant, is easy to be accumulated in aquatic products and poses a great threat to human health. In this work, we proposed a mix-to-read, label-free, and robust assay for detecting mercury pollution in aquatic products by engineering a ratiometric-enhanced G-quadruplex probe. The transformation from the G-quadruplex to a hairpin-like structure allows us to confer a ratiometric and leveraged response to Hg2+, amplifying the signal-to-background ratio for Hg2+ detection. Hg2+ response was further improved by screening parallel- and antiparallel-, single-, and multiple-stranded G-quadruplex structures. Compared to the common aptamer probes, the ratiometric-enhanced G-quadruplex probe increased the sensitivity for Hg2+ detection by 4.7 times. This proposed sensing system allowed a simple and one-tube homogenous detection of Hg2+ at room temperature using a single unlabeled DNA sequence. Its application for Hg2+ detection in fish and shrimp conferred satisfactory recovery rates ranging from 98.5 to 105.9%. The label-free and mix-to-read assay is promising for the onsite detection of mercury pollution and facilitating food safety of aquatic products.
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Affiliation(s)
- Yanping Wu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yuxi Yue
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Mi Zhou
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kai Zhong
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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21
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Wu Y, Shi Y, Deng S, Wu C, Deng R, He G, Zhou M, Zhong K, Gao H. Metal-induced G-quadruplex polymorphism for ratiometric and label-free detection of lead pollution in tea. Food Chem 2020; 343:128425. [PMID: 33127221 DOI: 10.1016/j.foodchem.2020.128425] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Lead pollution are critical concerns for food safety and human health. Herein, a ratiometric metal-induced G-quadruplex polymorphism was introduced to construct aptamer probes, enabling label-free and ratiometric detection of lead in tea, thus is promising for on-site detection of lead pollution. The key feature of the aptamer probe is the synergistic utilization of the dual-wavelength fluorescent signal outputs from a G-quadruplex specific dye and a DNA intercalation dye under a single-wavelength excitation, leading to a more stable and reliable recognition of Pb2+ than that of analyses based on single fluorescent reporter. The aptamer probe allowed to a mix-and-read, rapid, cost-effective detection of Pb2+ with high specificity and accuracy. Pb2+ analysis in tap water and tea exhibited good performance with recovery rates of 92.3%-109.0%. The adoption of ratiometric metal-induced G-quadruplex polymorphism would be a compelling design strategy for constructing robust aptasensor, facilitating the translation of aptamer for food safety control.
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Affiliation(s)
- Yanping Wu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Yachen Shi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China.
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Mi Zhou
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Kai Zhong
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China.
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22
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Cao Y, Yang L, Ding P, Li W, Pei R. Ligand Selectivity by Inserting GCGC‐Tetrads into G‐Quadruplex Structures. Chemistry 2020; 26:14730-14737. [DOI: 10.1002/chem.202003004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/22/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface Division of Nanobiomedicine Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences Suzhou 215123 P. R. China
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23
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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24
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Paudel BP, Moye AL, Abou Assi H, El-Khoury R, Cohen SB, Holien JK, Birrento ML, Samosorn S, Intharapichai K, Tomlinson CG, Teulade-Fichou MP, González C, Beck JL, Damha MJ, van Oijen AM, Bryan TM. A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution. eLife 2020; 9:56428. [PMID: 32723475 PMCID: PMC7426096 DOI: 10.7554/elife.56428] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is only through the large conformational change of translocation following synthesis that the G-quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4 stabilization with either small molecule ligands or by chemical modification does not always inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a parallel G-quadruplex resolvase.
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Affiliation(s)
- Bishnu P Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Aaron Lavel Moye
- Children's Medical Research Institute, University of Sydney, Westmead, Australia
| | - Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, Canada
| | | | - Scott B Cohen
- Children's Medical Research Institute, University of Sydney, Westmead, Australia
| | - Jessica K Holien
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Australia
| | - Monica L Birrento
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Siritron Samosorn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - Kamthorn Intharapichai
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, Japan
| | | | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, Madrid, Spain
| | - Jennifer L Beck
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, Australia
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25
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Cao Y, Li W, Gao T, Ding P, Pei R. One Terminal Guanosine Flip of Intramolecular Parallel G-Quadruplex: Catalytic Enhancement of G-Quadruplex/Hemin DNAzymes. Chemistry 2020; 26:8631-8638. [PMID: 32428287 DOI: 10.1002/chem.202001462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/13/2020] [Indexed: 11/09/2022]
Abstract
Numerous studies have shown compelling evidence that incorporation of an inversion of polarity site (IPS) in G-rich sequences can affect the topological and structural characteristics of G-quadruplexes (G4s). Herein, the influence of IPS on the formation of a previously studied intramolecular parallel G4 of d(G3 TG3 TG3 TG3 ) (TTT) and its stacked higher-order structures is explored. Insertion of 3'-3' or 5'-5' IPS did not change the parallel folding pattern of TTT. However, both the species and position of the IPS in TTT have a significant impact on the G4 stability and end-stacking through the alteration of G4-G4 interfaces properties. The data demonstrate that one base flip in each terminal G-tetrad can stabilize parallel G4s and facilitate intermolecular packing of monomeric G4s. Such modifications can also enhance the fluorescence and enzymatic performances by promoting interactions between parallel G4s with N-methyl mesoporphyrin IX (NMM) and hemin, respectively.
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Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Tian Gao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
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26
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Wang J, Wu Y, Wu Q, Li L, Wang Y, Yang H. Highly sensitive detection of melamine in milk samples based on N-methylmesoporphyrin IX/G-quadruplex structure. Microchem J 2020. [DOI: 10.1016/j.microc.2020.104751] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Butkus JM, Pytko KG, Stead CE, Basu S. Binding of quadruplex DNA to nickel and zinc complexes monitored by surface-enhanced raman and fluorescence spectroscopy. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Martone J, Mariani D, Santini T, Setti A, Shamloo S, Colantoni A, Capparelli F, Paiardini A, Dimartino D, Morlando M, Bozzoni I. SMaRT lncRNA controls translation of a G-quadruplex-containing mRNA antagonizing the DHX36 helicase. EMBO Rep 2020; 21:e49942. [PMID: 32337838 PMCID: PMC7271651 DOI: 10.15252/embr.201949942] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Guanine‐quadruplexes (G4) included in RNA molecules exert several functions in controlling gene expression at post‐transcriptional level; however, the molecular mechanisms of G4‐mediated regulation are still poorly understood. Here, we describe a regulatory circuitry operating in the early phases of murine muscle differentiation in which a long non‐coding RNA (SMaRT) base pairs with a G4‐containing mRNA (Mlx‐γ) and represses its translation by counteracting the activity of the DHX36 RNA helicase. The time‐restricted, specific effect of lnc‐SMaRT on the translation of Mlx‐γ isoform modulates the general subcellular localization of total MLX proteins, impacting on their transcriptional output and promoting proper myogenesis and mature myotube formation. Therefore, the circuitry made of lnc‐SMaRT, Mlx‐γ, and DHX36 not only plays an important role in the control of myogenesis but also unravels a molecular mechanism where G4 structures and G4 unwinding activities are regulated in living cells.
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Affiliation(s)
- Julie Martone
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Davide Mariani
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Sama Shamloo
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Francesca Capparelli
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | | | - Dacia Dimartino
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology, Charles Darwin, Sapienza University of Rome, Rome, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
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Tateishi-Karimata H, Sugimoto N. Chemical biology of non-canonical structures of nucleic acids for therapeutic applications. Chem Commun (Camb) 2020; 56:2379-2390. [PMID: 32022004 DOI: 10.1039/c9cc09771f] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA forms not only the canonical duplex structure but also non-canonical structures. Most potential sequences that induce the formation of non-canonical structures are present in disease-related genes. Interestingly, biological reactions are inhibited or dysregulated by non-canonical structure formation in disease-related genes. To control biological reactions, methods for inducing the formation of non-canonical structures have been developed using small molecules and oligonucleotides. In this feature article, we review biological reactions such as replication, transcription, and reverse transcription controlled by non-canonical DNA structures formed by disease-related genes. Furthermore, we discuss recent studies aimed at developing methods for regulating these biological reactions using drugs targeting the DNA structure.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
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30
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Zhang L, Liu X, Lu S, Liu J, Zhong S, Wei Y, Bing T, Zhang N, Shangguan D. Thiazole Orange Styryl Derivatives as Fluorescent Probes for G-Quadruplex DNA. ACS APPLIED BIO MATERIALS 2020; 3:2643-2650. [DOI: 10.1021/acsabm.9b01243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Lingling Zhang
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Guangxi Medical University, No. 22, Shuangyong Road, Nanning 530021, Guangxi, PR China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Lu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilong Zhong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yongbiao Wei
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Guangxi Medical University, No. 22, Shuangyong Road, Nanning 530021, Guangxi, PR China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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31
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Perenon M, Bonnet H, Lavergne T, Dejeu J, Defrancq E. Surface plasmon resonance study of the interaction of N-methyl mesoporphyrin IX with G-quadruplex DNA. Phys Chem Chem Phys 2020; 22:4158-4164. [PMID: 32039427 DOI: 10.1039/c9cp06321h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Surface plasmon resonance (SPR) was used to investigate the interaction between N-methyl mesoporphyrin IX (NMM) and different G-quadruplex (G4) topologies. The study was associated with circular dichroism analysis (CD) to assess the topology of the G4s when they interacted with NMM. We demonstrate the high selectivity of NMM for the parallel G4 structure with a dissociation constant at least ten times lower than those of other G4 topologies. We also confirm the ability of NMM to shift the G4 conformation from both the hybrid and antiparallel topologies toward the parallel structure.
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Affiliation(s)
- M Perenon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - H Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - T Lavergne
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - J Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - E Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
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Ma L, Han X, Xia L, Qu F, Kong RM. A label-free G-quadruplex-based fluorescence assay for sensitive detection of alkaline phosphatase with the assistance of Cu 2. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117607. [PMID: 31654846 DOI: 10.1016/j.saa.2019.117607] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 08/07/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
The level of alkaline phosphate (ALP) is a significant biomarker index in organism. In this work, a label-free and sensitive G-quadruplex fluorescence assay for monitoring ALP activity has been developed with the assistance of Cu2+ based on the competitive binding effect between pyrophosphate (PPi) and G-quadruplex-N-methylmesoporphyrin (G4/NMM) complex to Cu2+. In the sensing assay, the G4/NMM complex is employed as a signal indicator, while the Cu2+ as a quencher and the PPi as recovery agent as well as the hydrolytic substance for ALP. In details, the fluorescence of the G4/NMM complex was efficiently quenched by introducing Cu2+ due to the proximal carboxylate groups of NMM coordinating with the Cu2+ as well as the unfolding of G-quadruplex by Cu2+, while the higher affinity between PPi and Cu2+ could lead to the fluorescence recovery. However, in the presence of ALP, the PPi was hydrolyzed to phosphate ions (Pi) which cannot integrate with Cu2+, resulting in the fluorescence quenching once again. Thus, a simple and facile way to inspect ALP has been exploited. The proposed assay shows a good linear relationship in the range from 0.5 to 100 U/L with the detection limit of 0.3 U/L. Moreover, the fabricated method is succeeded in detecting ALP in human serum samples, indicating the potential as a profitable candidate in biological and biomedical application.
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Affiliation(s)
- Lin Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu Shandong, 273165, PR China
| | - Xue Han
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu Shandong, 273165, PR China
| | - Lian Xia
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu Shandong, 273165, PR China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu Shandong, 273165, PR China
| | - Rong-Mei Kong
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu Shandong, 273165, PR China.
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Imperatore JA, McAninch DS, Valdez-Sinon AN, Bassell GJ, Mihailescu MR. FUS Recognizes G Quadruplex Structures Within Neuronal mRNAs. Front Mol Biosci 2020; 7:6. [PMID: 32118033 PMCID: PMC7018707 DOI: 10.3389/fmolb.2020.00006] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fused in sarcoma (FUS), identified as the heterogeneous nuclear ribonuclear protein P2, is expressed in neuronal and non-neuronal tissue, and among other functions, has been implicated in messenger RNA (mRNA) transport and possibly local translation regulation. Although FUS is mainly localized to the nucleus, in the neurons FUS has also been shown to localize to the post-synaptic density, as well as to the pre-synapse. Additionally, the FUS deletion in cultured hippocampal cells results in abnormal spine and dendrite morphology. Thus, FUS may play a role in synaptic function regulation, mRNA localization, and local translation. Many dendritic mRNAs have been shown to form G quadruplex structures in their 3'-untranslated region (3'-UTR). Since FUS contains three arginine-glycine-glycine (RGG) boxes, an RNA binding domain shown to bind with high affinity and specificity to RNA G quadruplex structures, in this study we hypothesized that FUS recognizes these structural elements in its neuronal mRNA targets. Two neuronal mRNAs found in the pre- and post-synapse are the post-synaptic density protein 95 (PSD-95) and Shank1 mRNAs, which encode for proteins involved in synaptic plasticity, maintenance, and function. These mRNAs have been shown to form 3'-UTR G quadruplex structures and were also enriched in FUS hydrogels. In this study, we used native gel electrophoresis and steady-state fluorescence spectroscopy to demonstrate specific nanomolar binding of the FUS C-terminal RGG box and of full-length FUS to the RNA G quadruplex structures formed in the 3'-UTR of PSD-95 and Shank1a mRNAs. These results point toward a novel mechanism by which FUS targets neuronal mRNA and given that these PSD-95 and Shank1 3'-UTR G quadruplex structures are also targeted by the fragile X mental retardation protein (FMRP), they raise the possibility that FUS and FMRP might work together to regulate the translation of these neuronal mRNA targets.
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Affiliation(s)
- Joshua A. Imperatore
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, United States
| | - Damian S. McAninch
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, United States
| | | | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, United States
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Imperatore JA, Then ML, McDougal KB, Mihailescu MR. Characterization of a G-Quadruplex Structure in Pre-miRNA-1229 and in Its Alzheimer's Disease-Associated Variant rs2291418: Implications for miRNA-1229 Maturation. Int J Mol Sci 2020; 21:ijms21030767. [PMID: 31991575 PMCID: PMC7037302 DOI: 10.3390/ijms21030767] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD), the most common age-related neurodegenerative disease, is associated with various forms of cognitive and functional impairment that worsen with disease progression. AD is typically characterized as a protein misfolding disease, in which abnormal plaques form due to accumulation of tau and β-amyloid (Aβ) proteins. An assortment of proteins is responsible for the processing and trafficking of Aβ, including sortilin-related receptor 1 (SORL1). Recently, a genome-wide association study of microRNA-related variants found that a single nucleotide polymorphism (SNP) rs2291418 within premature microRNA-1229 (pre-miRNA-1229) is significantly associated with AD. Moreover, the levels of the mature miRNA-1229-3p, which has been shown to regulate the SORL1 translation, are increased in the rs2291418 pre-miRNA-1229 variant. In this study we used various biophysical techniques to show that pre-miRNA-1229 forms a G-quadruplex secondary structure that coexists in equilibrium with the canonical hairpin structure, potentially controlling the production of the mature miR-1229-3p, and furthermore, that the AD-associated SNP rs2291418 pre-miR-1229 changes the equilibrium between these structures. Thus, the G-quadruplex structure we identified within pre-miRNA-1229 could potentially act as a novel therapeutic target in AD.
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Yett A, Lin LY, Beseiso D, Miao J, Yatsunyk LA. N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA. J PORPHYR PHTHALOCYA 2019; 23:1195-1215. [PMID: 34385812 PMCID: PMC8356643 DOI: 10.1142/s1088424619300179] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.
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Affiliation(s)
- Ariana Yett
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Yingqi Lin
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Dana Beseiso
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Liliya A. Yatsunyk
- Correspondence to: Liliya A. Yatsunyk, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA. tel.: 610-328-8558,
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36
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Yang F, Li X, Li J, Xiang Y, Yuan R. Target-triggered activation of rolling circle amplification for label-free and sensitive fluorescent uracil-DNA glycosylase activity detection and inhibition. Talanta 2019; 204:812-816. [DOI: 10.1016/j.talanta.2019.06.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 01/17/2023]
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Zuffo M, Guédin A, Leriche ED, Doria F, Pirota V, Gabelica V, Mergny JL, Freccero M. More is not always better: finding the right trade-off between affinity and selectivity of a G-quadruplex ligand. Nucleic Acids Res 2019; 46:e115. [PMID: 29986058 PMCID: PMC6212845 DOI: 10.1093/nar/gky607] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022] Open
Abstract
Guanine-rich nucleic acid sequences can fold into four-stranded G-quadruplex (G4) structures. Despite growing evidence for their biological significance, considerable work still needs to be done to detail their cellular occurrence and functions. Herein, we describe an optimized core-extended naphthalene diimide (cex-NDI) to be exploited as a G4 light-up sensor. The sensing mechanism relies on the shift of the aggregate-monomer equilibrium towards the bright monomeric state upon G4 binding. In contrast with the majority of other ligands, this novel cex-NDI is able to discriminate among G4s with different topologies, with a remarkable fluorescent response for the parallel ones. We investigate this sensing by means of biophysical methods, comparing the lead compound to a non-selective analogue. We demonstrate that mitigating the affinity of the binding core for G4s results in an increased selectivity and sensitivity of the fluorescent response. This is achieved by replacing positively charged substituents with diethylene glycol (DEG) side chains. Remarkably, the limit of detection values obtained for parallel G4s are more than one order of magnitude lower than those of the parallel-selective ligand N-methyl mesoporphyrin IX (NMM). Interestingly, the classical fluorescent intercalator displacement (FID) assay failed to reveal binding of cex-NDI to G4 because of the presence a ternary complex (G4-TO-cex-NDI) revealed by electrospray-MS. Our study thus provides a rational basis to design or modify existent scaffolds to redirect the binding preference of G4 ligands.
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Affiliation(s)
- Michela Zuffo
- Dipartimento di Chimica, Università di Pavia, Pavia 27100, Italy
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac 33607, France
| | - Emma-Dune Leriche
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac 33607, France
| | - Filippo Doria
- Dipartimento di Chimica, Università di Pavia, Pavia 27100, Italy
| | - Valentina Pirota
- Dipartimento di Chimica, Università di Pavia, Pavia 27100, Italy
| | - Valérie Gabelica
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac 33607, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac 33607, France.,Institute of Biophysics, AS CR, Brno 61265, Czech Republic
| | - Mauro Freccero
- Dipartimento di Chimica, Università di Pavia, Pavia 27100, Italy
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Li Q, Liu Z, Zhou D, Pan J, Liu C, Chen J. A cascade toehold-mediated strand displacement strategy for label-free and sensitive non-enzymatic recycling amplification detection of the HIV-1 gene. Analyst 2019; 144:2173-2178. [PMID: 30768078 DOI: 10.1039/c8an02340a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this work, a label-free fluorescence biosensor for simple detection of the HIV-1 gene was proposed by using toehold-mediated strand displacement reactions (TMSDRs) combined with a non-enzymatic target recycling amplification strategy. In this system, two TMSDRs were used. In the presence of the HIV-1 gene, an autocatalytic DNA machine can be activated. This leads to the generation of numerous free G-rich sequences, which can associate with a fluorescent dye N-methylmesoporphyrin IX (NMM) to yield an amplified fluorescence signal for the target detection. This sensing platform showed a high sensitivity towards the HIV-1 gene with a detection limit as low as 1.9 pM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits an excellent selectivity for the HIV-1 gene compared with other interference DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the HIV-1 gene in a real biological sample with satisfactory results, suggesting that this method is promising for simple and early clinical diagnosis of HIV infection. Thanks to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a universal platform for the detection of other genes by substituting the target-recognition element.
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Affiliation(s)
- Qiong Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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39
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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40
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DNA-MnO2 nanosheets as washing- and label-free platform for array-based differentiation of cell types. Anal Chim Acta 2019; 1056:1-6. [DOI: 10.1016/j.aca.2019.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/28/2018] [Accepted: 01/08/2019] [Indexed: 01/05/2023]
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41
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Cao Y, Kuang Y, Yang L, Ding P, Pei R. Construction of One- and Two-Dimensional Nanostructures by the Sequential Assembly of Quadruplex DNA Scaffolds. Biomacromolecules 2019; 20:2207-2217. [DOI: 10.1021/acs.biomac.9b00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ye Kuang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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42
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Yang L, Ding P, Luo Y, Wang J, Lv H, Li W, Cao Y, Pei R. Exploration of Catalytic Nucleic Acids on Porphyrin Metalation and Peroxidase Activity by in Vitro Selection of Aptamers for N-Methyl Mesoporphyrin IX. ACS COMBINATORIAL SCIENCE 2019; 21:83-89. [PMID: 30602113 DOI: 10.1021/acscombsci.8b00129] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To develop a novel light-up probe and DNAzyme, we selected aptamers for N-methyl mesoporphyrin IX (NMM), a common fluorogenic analogue of coenzyme hemin, by a modified affinity chromatography-based systematic evolution of ligands by exponential enrichment (SELEX). Two truncated aptamers Nm1 and Nm2 with low micromolar dissociation constants (0.75 and 13.27 μM) were obtained after 11 rounds of selection and the final minimized 39-mer aptamer Nm2.1 showed 24-fold fluorescence enhancement for NMM at saturated concentration. Study of the interactions between aptamers and other porphyrin compounds by circular dichroism (CD) and absorption spectroscopy showed that Nm1 mainly assembled as a stem-loop structure, which exhibited a catalytic activity for the metal insertion reaction of mesoporphyrin IX with 3.3-fold rate enhancement. In contrast, the G-rich Nm2 and Nm2.1 were likely to form G-quadruplexes in the presence of alkali metal cations (K+ and Na+), which displayed excellent peroxidase activity exhibiting 19-fold higher catalytic efficiency than hemin alone. The selected aptamers could therefore be used as novel light-up fluorescent probes and DNAzymes by pairing with porphyrin compounds that have potential to construct sensors for various applications.
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Affiliation(s)
- Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Haiyin Lv
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- School of Nano Technology and Nano Bionics, University of Science and Technology of China, Hefei 230026, China
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Zhou W, Yu Z, Ma G, Jin T, Li Y, Fan L, Li X. Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation. Analyst 2019; 144:2284-2290. [DOI: 10.1039/c8an02430h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).
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Affiliation(s)
- Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Tian Jin
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
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44
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Yeasmin Khusbu F, Zhou X, Chen H, Ma C, Wang K. Thioflavin T as a fluorescence probe for biosensing applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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45
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Asamitsu S, Bando T, Sugiyama H. Ligand Design to Acquire Specificity to Intended G-Quadruplex Structures. Chemistry 2018; 25:417-430. [PMID: 30051593 DOI: 10.1002/chem.201802691] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/14/2018] [Indexed: 12/17/2022]
Abstract
A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.
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Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto, 606-8501, Japan
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46
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Li X, Tang X, Chen X, Qu B, Lu L. Label-free and enzyme-free fluorescent isocarbophos aptasensor based on MWCNTs and G-quadruplex. Talanta 2018; 188:232-237. [DOI: 10.1016/j.talanta.2018.05.092] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/22/2018] [Accepted: 05/27/2018] [Indexed: 01/08/2023]
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47
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Genome-wide analysis of regulatory G-quadruplexes affecting gene expression in human cytomegalovirus. PLoS Pathog 2018; 14:e1007334. [PMID: 30265731 PMCID: PMC6179306 DOI: 10.1371/journal.ppat.1007334] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/10/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
G-quadruplex (G4), formed by repetitive guanosine-rich sequences, is known to play various key regulatory roles in cells. Herpesviruses containing a large double-stranded DNA genome show relatively higher density of G4-forming sequences in their genomes compared to human and mouse. However, it remains poorly understood whether all of these sequences form G4 and how they play a role in the virus life cycle. In this study, we performed genome-wide analyses of G4s present in the putative promoter or gene regulatory regions of a 235-kb human cytomegalovirus (HCMV) genome and investigated their roles in viral gene expression. We evaluated 36 putative G4-forming sequences associated with 20 genes for their ability to form G4 and for the stability of G4s in the presence or absence of G4-stabilizing ligands, by circular dichroism and melting temperature analyses. Most identified sequences formed a stable G4; 28 sequences formed parallel G4s, one formed an antiparallel G4, and four showed mixed conformations. However, when we assessed the effect of G4 on viral promoters by cloning the 20 putative viral promoter regions containing 36 G4-forming sequences into the luciferase reporter and monitoring the expression of luciferase reporter gene in the presence of G4-stabilizing chemicals, we found that only 9 genes were affected by G4 formation. These results revealed promoter context-dependent gene suppression by G4 formation. Mutational analysis of two potential regulatory G4s also demonstrated gene suppression by the sequence-specific G4 formation. Furthermore, the analysis of a mutant virus incapable of G4 formation in the UL35 promoter confirmed promoter regulation by G4 in the context of virus infection. Our analyses provide a platform for assessing G4 functions at the genomic level and demonstrate the properties of the HCMV G4s and their regulatory roles in viral gene expression.
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An Aptamer-Based Biosensor for Direct, Label-Free Detection of Melamine in Raw Milk. SENSORS 2018; 18:s18103227. [PMID: 30257498 PMCID: PMC6210019 DOI: 10.3390/s18103227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023]
Abstract
Melamine, a nitrogen-rich compound, has been used as a food and milk additive to falsely increase the protein content. However, melamine is toxic, and high melamine levels in food or in milk can cause kidney and urinary problems, or even death. Hence, the detection of melamine in food and milk is desirable, for which numerous detection methods have been developed. Several methods have successfully detected melamine in raw milk; however, they require a sample preparation before the analyses. This study aimed to develop an aptamer-DNAzyme conjugated biosensor for label-free detection of melamine, in raw milk, without any sample preparation. An aptamer-DNAzyme conjugated biosensor was developed via screening using microarray analysis to identify the candidate aptamers followed by an optimization, to reduce the background noise and improve the aptamer properties, thereby, enhancing the signal-to-noise (S/N) ratio of the screened biosensor. The developed biosensor was evaluated via colorimetric detection and tested with raw milk without any sample preparation, using N-methylmesoporphyrin IX for fluorescence detection. The biosensor displayed significantly higher signal intensity at 2 mM melamine (S/N ratio, 20.2), which was sufficient to detect melamine at high concentrations, in raw milk.
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Halder D, Purkayastha P. A flavonol that acts as a potential DNA minor groove binder as also an efficient G-quadruplex loop binder. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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50
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Ding B, Liu C, Wu Q, Wang Y, Li L, Yang H. A Label-free and Highly Sensitive Fluorescence Strategy for Mercury Ion Detection Based on Exonuclease III-aided Recycling Amplification. ANAL SCI 2018. [PMID: 29526891 DOI: 10.2116/analsci.34.259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we describe a simple and highly sensitive fluorescence strategy of mercury ions based on exonuclease III (Exo III)-aided target recycling amplification to ensure sensitivity. With an ultra high sensitivity (1 pM), our strategy has been simple and cost-effective, which does not need any artificial modification fluorescence groups, and can be carried out in a pot. It also shows excellent selectivity. Therefore, our new method provides an effective platform for mercury-ion detection.
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Affiliation(s)
- Baomiao Ding
- Jingchu Food Research and Development Center, College of Life Science, Yangtze University
| | - Chenguang Liu
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
| | - Qinghua Wu
- Jingchu Food Research and Development Center, College of Life Science, Yangtze University
| | - Yun Wang
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
| | - Li Li
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
| | - Hualin Yang
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
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