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Chakraborty G, Balinin K, Villar-Guerra RD, Emondts M, Portale G, Loznik M, Niels Klement WJ, Zheng L, Weil T, Chaires JB, Herrmann A. Supramolecular DNA-based catalysis in organic solvents. iScience 2024; 27:109689. [PMID: 38706840 PMCID: PMC11067378 DOI: 10.1016/j.isci.2024.109689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/04/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
The distinct folding accompanied by its polymorphic character renders DNA G-quadruplexes promising biomolecular building blocks to construct novel DNA-based and supramolecular assemblies. However, the highly polar nature of DNA limits the use of G-quadruplexes to water as a solvent. In addition, the archetypical G-quadruplex fold needs to be stabilized by metal-cations, which is usually a potassium ion. Here, we show that a noncovalent PEGylation process enabled by electrostatic interactions allows the first metal-free G-quadruplexes in organic solvents. Strikingly, incorporation of an iron-containing porphyrin renders the self-assembled metal-free G-quadruplex catalytically active in organic solvents. Hence, these "supraG4zymes" enable DNA-based catalysis in organic media. The results will allow the broad utilization of DNA G-quadruplexes in nonaqueous environments.
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Affiliation(s)
- Gurudas Chakraborty
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Konstantin Balinin
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Rafael del Villar-Guerra
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Meike Emondts
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Giuseppe Portale
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Mark Loznik
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Wiebe Jacob Niels Klement
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Lifei Zheng
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
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2
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Chang T, Li G, Chang D, Amini R, Zhu X, Zhao T, Gu J, Li Z, Li Y. An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function. Angew Chem Int Ed Engl 2023; 62:e202310941. [PMID: 37648674 DOI: 10.1002/anie.202310941] [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: 07/31/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.
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Affiliation(s)
- Tianjun Chang
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Guangping Li
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Xiaoni Zhu
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Tongqian Zhao
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Zhongping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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3
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Mao X, Qiu D, Wei S, Zhang X, Lei J, Mergny JL, Ju H, Zhou J. A Double Hemin Bonded G-Quadruplex Embedded in Metal-Organic Frameworks for Biomimetic Cascade Reaction. ACS APPLIED MATERIALS & INTERFACES 2022; 14:54598-54606. [PMID: 36459081 DOI: 10.1021/acsami.2c18473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Biocatalytic transformations in living cells, such as enzymatic cascades, function effectively in spatially confined microenvironments. However, mimicking enzyme catalytic cascade processes is challenging. Herein, we report a new dual-Hemin-G-quadruplex (dHemin-G4) DNAzyme with high catalytic activity over noncovalent G4/Hemin and monocovalent counterparts (G4-Hemin and Hemin-G4) by covalently linking hemin to both ends of an intramolecular G4. We use MAF-7, a hydrophilic metal-organic framework (MOF), as the protecting scaffold to integrate a biocatalytic cascade consisting of dHemin-G4 DNAzyme and glucose oxidase (GOx), by a simple and mild method with a single-step encapsulation of both enzymes. Such a MAF-7-confined cascade system shows superior activity over not only traditional G4/Hemin but also other MOFs (ZIF-8 and ZIF-90), which was mainly attributed to high-payload enzyme packaging. Notably, the introduction of hydrophilic G4 allows to avoid the accumulation of hydrophobic hemin on the surface of MAF-7, which decreases cascade biocatalytic activity. Furthermore, MAF-7 as protective coatings endowed the enzyme with excellent recyclability and good operational stability in harsh environments, including elevated temperature, urea, protease, and organic solvents, extending its practical application in biocatalysis. In addition, the incorporated enzymes can be replaced on demand to broaden the scope of catalytic substrates. Taking advantages of these features, the feasibility of dHemin-G4/GOx@MAF-7 systems for biosensing was demonstrated. This study is conducive to devise efficient and stable enzyme catalytic cascades to facilitate applications in biosensing and industrial processes.
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Affiliation(s)
- Xuanxiang Mao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Shijiong Wei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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4
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Chen Y, Qiu D, Zhang X, Liu Y, Cheng M, Lei J, Mergny JL, Ju H, Zhou J. Highly Sensitive Biosensing Applications of a Magnetically Immobilizable Covalent G-Quadruplex-Hemin DNAzyme Catalytic System. Anal Chem 2022; 94:2212-2219. [PMID: 35050586 DOI: 10.1021/acs.analchem.1c04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplex/hemin (G4/hemin) DNAzymes are biosensing systems, but their application remains limited by an overall low activity and a rather high level of unwarranted background reactions. Here, these issues were addressed through the rational design of F3T-azaC-hemin, a G4-based construct in which the hemin is covalently linked to the G4 core and its binding site flanked with a nucleotide activator, here d(T-azaC). This design led to a G4-DNAzyme whose performances have been ca. 150-fold increased compared to the parent G4-based system. The utility of F3T-azaC-hemin was demonstrated here through the ultrasensitive chemiluminescent detection of miRNA-221. The limit of detection (LOD) has been decreased to the femtomolar range, making it a new and highly efficient molecular tool in the biosensing technology field.
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Affiliation(s)
- Yun Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex 91128, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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5
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Ramos-Soriano J, Galan MC. Photoresponsive Control of G-Quadruplex DNA Systems. JACS AU 2021; 1:1516-1526. [PMID: 34723256 PMCID: PMC8549047 DOI: 10.1021/jacsau.1c00283] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 05/14/2023]
Abstract
G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.
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Affiliation(s)
- Javier Ramos-Soriano
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - M Carmen Galan
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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6
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Chang T, He S, Amini R, Li Y. Functional Nucleic Acids Under Unusual Conditions. Chembiochem 2021; 22:2368-2383. [PMID: 33930229 DOI: 10.1002/cbic.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/24/2021] [Indexed: 02/06/2023]
Abstract
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.
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Affiliation(s)
- Tianjun Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, P. R. China
| | - Sisi He
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen, 518055, Guangdong, P. R. China
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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7
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Shumayrikh NM, Warren JJ, Bennet AJ, Sen D. A heme•DNAzyme activated by hydrogen peroxide catalytically oxidizes thioethers by direct oxygen atom transfer rather than by a Compound I-like intermediate. Nucleic Acids Res 2021; 49:1803-1815. [PMID: 33476369 PMCID: PMC7913675 DOI: 10.1093/nar/gkab007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Hemin [Fe(III)-protoporphyrin IX] is known to bind tightly to single-stranded DNA and RNA molecules that fold into G-quadruplexes (GQ). Such complexes are strongly activated for oxidative catalysis. These heme•DNAzymes and ribozymes have found broad utility in bioanalytical and medicinal chemistry and have also been shown to occur within living cells. However, how a GQ is able to activate hemin is poorly understood. Herein, we report fast kinetic measurements (using stopped-flow UV-vis spectrophotometry) to identify the H2O2-generated activated heme species within a heme•DNAzyme that is active for the oxidation of a thioether substrate, dibenzothiophene (DBT). Singular value decomposition and global fitting analysis was used to analyze the kinetic data, with the results being consistent with the heme•DNAzyme's DBT oxidation being catalyzed by the initial Fe(III)heme-H2O2 complex. Such a complex has been predicted computationally to be a powerful oxidant for thioether substrates. In the heme•DNAzyme, the DNA GQ enhances both the kinetics of formation of the active intermediate as well as the oxidation step of DBT by the active intermediate. We show, using both stopped flow spectrophotometry and EPR measurements, that a classic Compound I is not observable during the catalytic cycle for thioether sulfoxidation.
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Affiliation(s)
- Nisreen M Shumayrikh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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8
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Proximity Ligation Assay Detection of Protein-DNA Interactions-Is There a Link between Heme Oxygenase-1 and G-quadruplexes? Antioxidants (Basel) 2021; 10:antiox10010094. [PMID: 33445471 PMCID: PMC7827836 DOI: 10.3390/antiox10010094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 01/12/2023] Open
Abstract
G-quadruplexes (G4) are stacked nucleic acid structures that are stabilized by heme. In cells, they affect DNA replication and gene transcription. They are unwound by several helicases but the composition of the repair complex and its heme sensitivity are unclear. We found that the accumulation of G-quadruplexes is affected by heme oxygenase-1 (Hmox1) expression, but in a cell-type-specific manner: hematopoietic stem cells (HSCs) from Hmox1−/− mice have upregulated expressions of G4-unwinding helicases (e.g., Brip1, Pif1) and show weaker staining for G-quadruplexes, whereas Hmox1-deficient murine induced pluripotent stem cells (iPSCs), despite the upregulation of helicases, have more G-quadruplexes, especially after exposure to exogenous heme. Using iPSCs expressing only nuclear or only cytoplasmic forms of Hmox1, we found that nuclear localization promotes G4 removal. We demonstrated that the proximity ligation assay (PLA) can detect cellular co-localization of G-quadruplexes with helicases, as well as with HMOX1, suggesting the potential role of HMOX1 in G4 modifications. However, this colocalization does not mean a direct interaction was detectable using the immunoprecipitation assay. Therefore, we concluded that HMOX1 influences G4 accumulation, but rather as one of the proteins regulating the heme availability, not as a rate-limiting factor. It is noteworthy that cellular G4–protein colocalizations can be quantitatively analyzed using PLA, even in rare cells.
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Abstract
Catalytic DNAs (DNAzymes) with peroxidase-like activity have great potential in bioanalytical chemistry [1], owing to numerous advantages that DNA enzymes offer over conventional protein enzymes, including structural simplicity, low cost, thermal stability, and straightforward handling and preparation. Maximizing the efficiency of the peroxidase activity of such DNAzymes is a subject in need of review. In this chapter, we discuss the optimal experimental conditions for the peroxidase activity of these DNAzymes and describe general procedures for their utilization.
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10
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Gray LT, Puig Lombardi E, Verga D, Nicolas A, Teulade-Fichou MP, Londoño-Vallejo A, Maizels N. G-quadruplexes Sequester Free Heme in Living Cells. Cell Chem Biol 2019; 26:1681-1691.e5. [PMID: 31668518 DOI: 10.1016/j.chembiol.2019.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/13/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
Heme is an essential cofactor for many enzymes, but free heme is toxic and its levels are tightly regulated. G-quadruplexes bind heme avidly in vitro, raising the possibility that they may sequester heme in vivo. If so, then treatment that displaces heme from quadruplexes is predicted to induce expression of genes involved in iron and heme homeostasis. Here we show that PhenDC3, a G-quadruplex ligand structurally unrelated to heme, displaces quadruplex-bound heme in vitro and alters transcription in cultured human cells, upregulating genes that support heme degradation and iron homeostasis, and most strikingly causing a 30-fold induction of heme oxidase 1, the key enzyme in heme degradation. We propose that G-quadruplexes sequester heme to protect cells from the pathophysiological consequences of free heme.
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Affiliation(s)
- Lucas T Gray
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Emilia Puig Lombardi
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris 75005, France
| | - Daniela Verga
- Institut Curie, Centre de Recherche, CNRS-UMR9187, INSERM-U1196, PSL Research University, Sorbonne Universités, Orsay 91405, France; CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay 91405, France
| | - Alain Nicolas
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris 75005, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, Centre de Recherche, CNRS-UMR9187, INSERM-U1196, PSL Research University, Sorbonne Universités, Orsay 91405, France; CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay 91405, France
| | - Arturo Londoño-Vallejo
- Institut Curie, Centre de Recherche, CNRS-UMR3244, PSL Research University, Paris 75005, France
| | - Nancy Maizels
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.
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11
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Ibrahim H, Mulyk P, Sen D. DNA G-Quadruplexes Activate Heme for Robust Catalysis of Carbene Transfer Reactions. ACS OMEGA 2019; 4:15280-15288. [PMID: 31552375 PMCID: PMC6751727 DOI: 10.1021/acsomega.9b02305] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/13/2019] [Indexed: 05/09/2023]
Abstract
Guanine-rich single-stranded DNAs and RNAs that fold into G-quadruplexes (GQs) are known to complex tightly with FeII-heme and FeIII-heme (hemin), ubiquitous cellular cofactors. Heme-GQ (DNA) complexes, known as heme·DNAzymes, are able to utilize hydrogen peroxide as an oxidant to vigorously catalyze a variety of one-electron (peroxidase) and two-electron (peroxygenase) oxidation reactions. Herein, we show that complexes of FeII-heme with GQs also robustly catalyze a mechanistically distinct reaction, carbene transfer to an alkene substrate. Significant enhancements were seen in both reaction kinetics and product turnover (∼180) relative to disaggregated FeII-heme in the absence of DNA or in the presence of other DNA folds, such as single-stranded or double-stranded DNA. Heme binds to GQs by end-stacking. Simple, intramolecularly folded GQs are unable to provide a complexly structured "distal side" environment to the bound heme; therefore, such DNAzymes do not display significant product stereoselectivity. However, intermolecular GQs with multiple pendant nucleotides show increasing stereoselectivity in addition to their enhanced catalytic rates. These results recapitulate the unique functional synergy and highlight the surprising catalytic versatility of complexes formed between heme and DNA/RNA GQs. Our findings suggest that heme·DNAzymes and heme·ribozymes may prove to be useful reagents for carbon-carbon bond forming "green" reactions carried out in vitro and likely within living cells.
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Affiliation(s)
- Hanadi Ibrahim
- Department
of Chemistry and Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- E-mail: (H.I.)
| | - Paul Mulyk
- Department
of Chemistry and Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department
of Chemistry and Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- E-mail: (D.S.)
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12
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O'Hagan MP, Morales JC, Galan MC. Binding and Beyond: What Else Can G-Quadruplex Ligands Do? European J Org Chem 2019. [DOI: 10.1002/ejoc.201900692] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”; Consejo Superior de Investigaciones Científicas (CSIC); PTS Granada; Avenida del Conocimiento 17 18016 Armilla, Granada Spain
| | - M. Carmen Galan
- School of Chemistry; University of Bristol; Cantock's Close BS8 1TS UK
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O'Hagan MP, Haldar S, Duchi M, Oliver TAA, Mulholland AJ, Morales JC, Galan MC. A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA. Angew Chem Int Ed Engl 2019; 58:4334-4338. [PMID: 30682233 PMCID: PMC6563076 DOI: 10.1002/anie.201900740] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Indexed: 11/14/2022]
Abstract
The polymorphic nature of G-quadruplex (G4) DNA structures points to a range of potential applications in nanodevices and an opportunity to control G4 in biological settings. Light is an attractive means for the regulation of oligonucleotide structure as it can be delivered with high spatiotemporal precision. However, surprisingly little attention has been devoted towards the development of ligands for G4 that allow photoregulation of G4 folding. We report a novel G4-binding chemotype derived from stiff-stilbene. Surprisingly however, whilst the ligand induces high stabilization in the potassium form of human telomeric DNA, it causes the unfolding of the same G4 sequence in sodium buffer. This effect can be reversed on demand by irradiation with 400 nm light through deactivation of the ligand by photo-oxidation. By fuelling the system with the photolabile ligand, the conformation of G4 DNA was switched five times.
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Affiliation(s)
| | - Susanta Haldar
- School of ChemistryUniversity of BristolCantock's CloseBS8 1TSUK
| | - Marta Duchi
- School of ChemistryUniversity of BristolCantock's CloseBS8 1TSUK
| | | | | | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”Consejo Superior de Investigaciones Científicas (CSIC)PTS GranadaAvenida del Conocimiento 1718016ArmillaGranadaSpain
| | - M. Carmen Galan
- School of ChemistryUniversity of BristolCantock's CloseBS8 1TSUK
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14
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O'Hagan MP, Haldar S, Duchi M, Oliver TAA, Mulholland AJ, Morales JC, Galan MC. A Photoresponsive Stiff‐Stilbene Ligand Fuels the Reversible Unfolding of G‐Quadruplex DNA. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900740] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Susanta Haldar
- School of ChemistryUniversity of Bristol Cantock's Close BS8 1TS UK
| | - Marta Duchi
- School of ChemistryUniversity of Bristol Cantock's Close BS8 1TS UK
| | | | | | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”Consejo Superior de Investigaciones Científicas (CSIC)PTS Granada Avenida del Conocimiento 17 18016 Armilla Granada Spain
| | - M. Carmen Galan
- School of ChemistryUniversity of Bristol Cantock's Close BS8 1TS UK
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15
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Kosman J, Żukowski K, Juskowiak B. Comparison of Characteristics and DNAzyme Activity of G4⁻Hemin Conjugates Obtained via Two Hemin Attachment Methods. Molecules 2018; 23:molecules23061400. [PMID: 29890720 PMCID: PMC6100319 DOI: 10.3390/molecules23061400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 11/16/2022] Open
Abstract
Two conjugation methods using different linkers were applied for the investigation of the spectral characteristics and activity of G-quadruplex (G4)–hemin conjugates. For this purpose, two G-quadruplex-forming DNA sequences were selected, and then conjugated to a hemin molecule via either amine coupling or a click reaction. The products obtained via these two methods differed in their chemistry and the length of the linker between the DNA and hemin molecules. Spectral characteristics revealed that both methods produced conjugates that were more thermally stable than G4/hemin complexes. Despite similar spectral characteristics, the conjugates obtained via these two methods differed in their DNAzyme activity. G4–hemin conjugates obtained through amine coupling exhibited higher activity than conjugates obtained through a click reaction. This was potentially due to the length and chemistry of the linker, which was 30 atoms long following the click reaction, but only six atoms long following amine coupling. A longer connector favors higher flexibility, and hence, reduces the binding of hemin with G4. The aromatic groups present in the linker obtained through the click reaction can also disturb the G4–hemin interaction. However, the conjugation of G4 DNA to hemin via the click reaction was connected to a higher yield, and did not require any sophisticated synthesis equipment.
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Affiliation(s)
- Joanna Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
| | - Krzysztof Żukowski
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
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16
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Sato H, Shimada N, Masuda T, Maruyama A. Allosteric Control of Peroxidase-Mimicking DNAzyme Activity with Cationic Copolymers. Biomacromolecules 2018; 19:2082-2088. [DOI: 10.1021/acs.biomac.8b00201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Hiroki Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Tsukuru Masuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
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17
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O'Hagan MP, Mergny JL, Waller ZAE. G-quadruplexes in Prague: A Bohemian Rhapsody. Biochimie 2018; 147:170-180. [PMID: 29452278 DOI: 10.1016/j.biochi.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 12/26/2022]
Abstract
The Sixth International Meeting on Quadruplex Nucleic Acids was held at the Hotel Internationale in Prague, Czech Republic from 31 May - 3 June 2017. A vibrant interdisciplinary community of over 300 scientists gathered to share their newest results in this exciting field and exchange ideas for further investigations.
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Affiliation(s)
- Michael Paul O'Hagan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS1 1TS, UK.
| | - Jean-Louis Mergny
- Univ. Bordeaux, ARNA Laboratory, Inserm U1212, CNRS UMR 5320, IECB, F-33600, France; Institute of Biophysics, AS CR, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Zoë Ann Ella Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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18
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Guo Y, Chen J, Cheng M, Monchaud D, Zhou J, Ju H. A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708964] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 160023 P. R. China
| | - David Monchaud
- Institut de Chimie Moléculaire; Université de Bourgogne (ICMUB); CNRS UMR6302; 21000 Dijon France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
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Guo Y, Chen J, Cheng M, Monchaud D, Zhou J, Ju H. A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme. Angew Chem Int Ed Engl 2017; 56:16636-16640. [DOI: 10.1002/anie.201708964] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 160023 P. R. China
| | - David Monchaud
- Institut de Chimie Moléculaire; Université de Bourgogne (ICMUB); CNRS UMR6302; 21000 Dijon France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing 210023 P. R. China
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Yu T, Zhou W, Liu J. Ultrasensitive DNAzyme-Based Ca 2+ Detection Boosted by Ethanol and a Solvent-Compatible Scaffold for Aptazyme Design. Chembiochem 2017; 19:31-36. [PMID: 29076615 DOI: 10.1002/cbic.201700498] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Indexed: 12/29/2022]
Abstract
Functional DNA includes aptamers and DNAzymes, and metal ions are often important for achieving the chemical functions of such DNA. Biosensors based on functional DNA have mainly been tested in aqueous buffers. By introducing organic solvents with much lower dielectric constants, the interaction between metal ions and DNA can be significantly enhanced, and this might affect the performance of DNA-based biosensors. In this work, the effect of ethanol on the activity of the EtNa DNAzyme was studied for Ca2+ detection. With 30 % ethanol, the sensor has a detection limit of 1.4 μm Ca2+ , which is a 16-fold improvement relative to that in water. This EtNa DNAzyme is unique because other tested DNAzymes are all inhibited by 50 % ethanol. Finally, by using the EtNa DNAzyme as a scaffold, the adenosine monophosphate (AMP) aptamer was inserted to construct an aptazyme, which allowed the measurement of AMP in ethanol. In summary, this study has reported the most sensitive DNA-based sensor for Ca2+ , and its sensitivity and selectivity can approach those of proteins or small-molecule ligands. This work also provides a way to measure aptamer binding in organic solvents.
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Affiliation(s)
- Tianmeng Yu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Wenhu Zhou
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, P.R. China
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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Giancola C, Montesarchio D. Not unusual, just different! Chemistry, biology and applications of G-quadruplex nucleic acids. Biochim Biophys Acta Gen Subj 2017; 1861:1201-1204. [PMID: 28578868 DOI: 10.1016/j.bbagen.2017.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/19/2017] [Accepted: 04/23/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Naples Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21,I-80126 Naples Italy
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