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Rossetto D, Cvjetan N, Walde P, Mansy SS. Protocellular Heme and Iron-Sulfur Clusters. Acc Chem Res 2024; 57:2293-2302. [PMID: 39099316 PMCID: PMC11339926 DOI: 10.1021/acs.accounts.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/10/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
ConspectusCentral to the quest of understanding the emergence of life is to uncover the role of metals, particularly iron, in shaping prebiotic chemistry. Iron, as the most abundant of the accessible transition metals on the prebiotic Earth, played a pivotal role in early biochemical processes and continues to be indispensable to modern biology. Here, we discuss our recent contributions to probing the plausibility of prebiotic complexes with iron, including heme and iron-sulfur clusters, in mediating chemistry beneficial to a protocell. Laboratory experiments and spectroscopic findings suggest plausible pathways, often facilitated by UV light, for the synthesis of heme and iron-sulfur clusters. Once formed, heme displays catalytic, peroxidase-like activity when complexed with amphiphiles. This activity could have been beneficial in two ways. First, heme could have catalytically removed a molecule (H2O2) that could have had degradative effects on a protocell. Second, heme could have helped in the synthesis of the building blocks of life by coupling the reduction of H2O2 with the oxidation of organic substrates. The necessity of amphiphiles to avoid the formation of inactive complexes of heme is telling, as the modern-day electron transport chain possesses heme embedded within a lipid membrane. Conversely, prebiotic iron-sulfur peptides have yet to be reported to partition into lipid membranes, nor have simple iron-sulfur peptides been found to be capable of participating in the synthesis of organic molecules. Instead, iron-sulfur peptides span a wide range of reduction potentials complementary to the reduction potentials of hemes. The reduction potential of iron-sulfur peptides can be tuned by the type of iron-sulfur cluster formed, e.g., [2Fe-2S] versus [4Fe-4S], or by the substitution of ligands to the metal center. Since iron-sulfur clusters easily form upon stochastic encounters between iron ions, hydrosulfide, and small organic molecules possessing a thiolate, including peptides, the likelihood of soluble iron-sulfur clusters seems to be high. What remains challenging to determine is if iron-sulfur peptides participated in early prebiotic chemistry or were recruited later when protocellular membranes evolved that were compatible with the exploitation of electron transfer for the storage of energy as a proton gradient. This problem mirrors in some ways the difficulty in deciphering the origins of metabolism as a whole. Chemistry that resembles some facets of extant metabolism must have transpired on the prebiotic Earth, but there are few clues as to how and when such chemistry was harnessed to support a (proto)cell. Ultimately, unraveling the roles of hemes and iron-sulfur clusters in prebiotic chemistry promises to deepen our understanding of the origins of life on Earth and aids the search for life elsewhere in the universe.
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Affiliation(s)
- Daniele Rossetto
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AlbertaT6G 2G2, Canada
- D-CIBIO, University of Trento, via Sommarive 9, Trento 38123, Italy
| | - Nemanja Cvjetan
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AlbertaT6G 2G2, Canada
- Department
of Materials, ETH Zürich, Leopold-Ruzicka-Weg 4, Zürich 8093, Switzerland
| | - Peter Walde
- Department
of Materials, ETH Zürich, Leopold-Ruzicka-Weg 4, Zürich 8093, Switzerland
| | - Sheref S. Mansy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AlbertaT6G 2G2, Canada
- D-CIBIO, University of Trento, via Sommarive 9, Trento 38123, Italy
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2
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Sahayasheela VJ, Sugiyama H. RNA G-quadruplex in functional regulation of noncoding RNA: Challenges and emerging opportunities. Cell Chem Biol 2024; 31:53-70. [PMID: 37909035 DOI: 10.1016/j.chembiol.2023.08.010] [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: 04/18/2023] [Revised: 07/12/2023] [Accepted: 08/22/2023] [Indexed: 11/02/2023]
Abstract
G-quadruplexes (G4s) are stable, noncanonical structures formed in guanine (G)-rich sequences of DNA/RNA. G4 structures are reported to play a regulatory role in various cellular processes and, recently, a considerable number of studies have attributed new biological functions to these structures, especially in RNA. Noncoding RNA (ncRNA), which does not translate into a functional protein, is widely expressed and has been shown to play a key role in shaping cellular activity. There has been growing evidence of G4 formation in several ncRNA classes, and it has been identified as a key part for diverse biological functions and physio-pathological contexts in neurodegenerative diseases and cancer. This review discusses RNA G4s (rG4s) in ncRNA, focusing on the molecular mechanism underlying its function. This review also aims to highlight potential and emerging opportunities to identify and target the rG4s in ncRNA to understand its function and, ultimately, treat many diseases.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan.
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3
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Cui Y, Zhang L, Liu J, Zhang T, Sugahara A, Momotake A, Yamamoto Y, Mao ZW, Tai H. Hydrogen Evolution of a Unique DNAzyme Composed of Cobalt-Protoporphyrin IX and G-Quadruplex DNA. CHEMSUSCHEM 2024; 17:e202301244. [PMID: 37681481 DOI: 10.1002/cssc.202301244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/09/2023]
Abstract
Molecular hydrogen (H2 ) is a clean and renewable fuel that has garnered significant interest in the search for alternatives to fossil fuels. Here, we constructed an artificial DNAzyme composed of cobalt-protoporphyrin IX (CoPP) and G-quadruplex DNA, possessing a unique H2 Oint ligand between the CoPP and G-quartet planes. We show for the first time that CoPP-DNAzyme catalyzes photo-induced H2 production under anaerobic conditions with a turnover number (TON) of 1229 ± 51 over 12 h at pH 6.05 and 10 °C. Compared with free-CoPP, complexation with G-quadruplex DNA resulted in a 4.7-fold increase in H2 production activity. The TON of the CoPP-DNAzyme revealed an optimal acid-base equilibrium with a pKa value of 7.60 ± 0.05, apparently originating from the equilibrium between Co(III)-H- and Co(I) states. Our results demonstrate that the H2 Oint ligand can augment and modulate the intrinsic catalytic activity of H2 production catalysts. These systems pave the way to using DNAzymes for H2 evolution in the direct conversion of solar energy to H2 from water.
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Affiliation(s)
- Yue Cui
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Li Zhang
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Jing Liu
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Taozhe Zhang
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Aya Sugahara
- Department of Chemistry, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Hulin Tai
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University Yanji, 133002, Jilin, China
- National Demonstration Centre for Experimental Chemistry Education, Yanbian University Yanji, 133002, Jilin, China
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4
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Abstract
Understanding how cells sense gases or gaseous solutes is a fundamental question in biology and is pivotal for the evolution of molecular and organismal life. In numerous organisms, gases can diffuse into cells, be transported, generated, and sensed. Controlling gases in the cellular environment is essential to prevent cellular and molecular damage due to interactions with gas-dependent free radicals. Consequently, the mechanisms governing acute gas sensing are evolutionarily conserved and have been experimentally elucidated in various organisms. However, the scientific literature on direct gas sensing is largely based on hemoprotein-based gasoreceptors (or sensors). As RNA-based G-quadruplex (G4) structures can also bind to heme, I propose that some ribozymes can act as gas-sensing riboceptors (ribonucleic acid receptors). Additionally, I present a few other ideas for non-heme metal ion- or metal cluster-based gas-sensing riboceptors. Studying riboceptors can help understand the evolutionary origins of cellular and gasocrine signaling.
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Affiliation(s)
- Savani Anbalagan
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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5
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Arnhold J. Inflammation-Associated Cytotoxic Agents in Tumorigenesis. Cancers (Basel) 2023; 16:81. [PMID: 38201509 PMCID: PMC10778456 DOI: 10.3390/cancers16010081] [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: 12/03/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic inflammatory processes are related to all stages of tumorigenesis. As inflammation is closely associated with the activation and release of different cytotoxic agents, the interplay between cytotoxic agents and antagonizing principles is highlighted in this review to address the question of how tumor cells overcome the enhanced values of cytotoxic agents in tumors. In tumor cells, the enhanced formation of mitochondrial-derived reactive species and elevated values of iron ions and free heme are antagonized by an overexpression of enzymes and proteins, contributing to the antioxidative defense and maintenance of redox homeostasis. Through these mechanisms, tumor cells can even survive additional stress caused by radio- and chemotherapy. Through the secretion of active agents from tumor cells, immune cells are suppressed in the tumor microenvironment and an enhanced formation of extracellular matrix components is induced. Different oxidant- and protease-based cytotoxic agents are involved in tumor-mediated immunosuppression, tumor growth, tumor cell invasion, and metastasis. Considering the special metabolic conditions in tumors, the main focus here was directed on the disturbed balance between the cytotoxic agents and protective mechanisms in late-stage tumors. This knowledge is mandatory for the implementation of novel anti-cancerous therapeutic approaches.
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Affiliation(s)
- Jürgen Arnhold
- Institute of Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
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6
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Deiana M, Andrés Castán J, Josse P, Kahsay A, Sánchez D, Morice K, Gillet N, Ravindranath R, Patel A, Sengupta P, Obi I, Rodriguez-Marquez E, Khrouz L, Dumont E, Abad Galán L, Allain M, Walker B, Ahn HS, Maury O, Blanchard P, Le Bahers T, Öhlund D, von Hofsten J, Monnereau C, Cabanetos C, Sabouri N. A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression. Nucleic Acids Res 2023; 51:6264-6285. [PMID: 37191066 PMCID: PMC10325911 DOI: 10.1093/nar/gkad365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Pierre Josse
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Abraha Kahsay
- Department of Integrative Medical Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Korentin Morice
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Natacha Gillet
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Ranjitha Ravindranath
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Indian Institute for Science Education and Research (IISER), Tirupati-517507, India
| | - Ankit Kumar Patel
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-901 87, Umeå, Sweden
| | - Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Lhoussain Khrouz
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Elise Dumont
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Laura Abad Galán
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Magali Allain
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Bright Walker
- Department of Chemistry, Kyung Hee University, Seoul, 02447, South Korea
| | - Hyun Seo Ahn
- Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
| | - Olivier Maury
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | | | - Tangui Le Bahers
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Daniel Öhlund
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-901 87, Umeå, Sweden
| | - Jonas von Hofsten
- Department of Integrative Medical Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Cyrille Monnereau
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Clément Cabanetos
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
- Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
- Building Blocks for FUture Electronics Laboratory (2BFUEL), IRL CNRS 2002, Yonsei University, Seoul, South Korea
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
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7
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Abstract
Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..
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Affiliation(s)
- Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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8
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Arnhold J. Host-Derived Cytotoxic Agents in Chronic Inflammation and Disease Progression. Int J Mol Sci 2023; 24:ijms24033016. [PMID: 36769331 PMCID: PMC9918110 DOI: 10.3390/ijms24033016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
At inflammatory sites, cytotoxic agents are released and generated from invading immune cells and damaged tissue cells. The further fate of the inflammation highly depends on the presence of antagonizing principles that are able to inactivate these host-derived cytotoxic agents. As long as the affected tissues are well equipped with ready-to-use protective mechanisms, no damage by cytotoxic agents occurs and resolution of inflammation is initiated. However, long-lasting and severe immune responses can be associated with the decline, exhaustion, or inactivation of selected antagonizing principles. Hence, cytotoxic agents are only partially inactivated and contribute to damage of yet-unperturbed cells. Consequently, a chronic inflammatory process results. In this vicious circle of permanent cell destruction, not only novel cytotoxic elements but also novel alarmins and antigens are liberated from affected cells. In severe cases, very low protection leads to organ failure, sepsis, and septic shock. In this review, the major classes of host-derived cytotoxic agents (reactive species, oxidized heme proteins and free heme, transition metal ions, serine proteases, matrix metalloproteases, and pro-inflammatory peptides), their corresponding protective principles, and resulting implications on the pathogenesis of diseases are highlighted.
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Affiliation(s)
- Jürgen Arnhold
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
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9
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Xiao X, Chen M, Zhang Y, Li L, Peng Y, Li J, Zhou W. Hemin-incorporating DNA nanozyme enabling catalytic oxygenation and GSH depletion for enhanced photodynamic therapy and synergistic tumor ferroptosis. J Nanobiotechnology 2022; 20:410. [PMID: 36109814 PMCID: PMC9479271 DOI: 10.1186/s12951-022-01617-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Photodynamic therapy (PDT) has emerged as a promising tumor treatment method via light-triggered generation of reactive oxygen species (ROS) to kill tumor cells. However, the efficacy of PDT is usually restricted by several biological limitations, including hypoxia, excess glutathione (GSH) neutralization, as well as tumor resistance. To tackle these issues, herein we developed a new kind of DNA nanozyme to realize enhanced PDT and synergistic tumor ferroptosis. The DNA nanozyme was constructed via rolling circle amplification, which contained repeat AS1411 G quadruplex (G4) units to form multiple G4/hemin DNAzymes with catalase-mimic activity. Both hemin, an iron-containing porphyrin cofactor, and chlorine e6 (Ce6), a photosensitizer, were facilely inserted into G4 structure with high efficiency, achieving in-situ catalytic oxygenation and photodynamic ROS production. Compared to other self-oxygen-supplying tools, such DNA nanozyme is advantageous for high biological stability and compatibility. Moreover, the nanostructure could achieve tumor cells targeting internalization and intranuclear transport of Ce6 by virtue of specific nucleolin binding of AS1411. The nanozyme could catalyze the decomposition of intracellular H2O2 into oxygen for hypoxia relief as evidenced by the suppression of hypoxia-inducible factor-1α (HIF-1α), and moreover, GSH depletion and cell ferroptosis were also achieved for synergistic tumor therapy. Upon intravenous injection, the nanostructure could effectively accumulate into tumor, and impose multi-modal tumor therapy with excellent biocompatibility. Therefore, by integrating the capabilities of O2 generation and GSH depletion, such DNA nanozyme is a promising nanoplatform for tumor PDT/ferroptosis combination therapy.
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Affiliation(s)
- Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Min Chen
- Department of Thoracic Surgery, The Second People's Hospital of Huaihua City, Huaihua, China
| | - Yuchen Zhang
- Department of Pharmacy, Yichun People's Hospital, Yichun, Jiangxi, China
| | - Liang Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Ying Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Junyu Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China.
| | - Wenhu Zhou
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China.
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10
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Teng Q, Wu H, Sun H, Liu Y, Wang H, Wang ZG. Switchable Enzyme-mimicking catalysts Self-Assembled from de novo designed peptides and DNA G-quadruplex/hemin complex. J Colloid Interface Sci 2022; 628:1004-1011. [PMID: 35970126 DOI: 10.1016/j.jcis.2022.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 01/02/2023]
Abstract
Reconstruction of enzymatic active site in an artificial system is key to achieving high catalytic efficiency. Herein, we report the self-assembly of the lysine-containing peptides with guanine-rich DNA and hemin to form peroxidase-mimicking active sites and catalytic nanoparticles. The DNA strand self-folds into a G-quadruplex structure that provides a supramolecular scaffold and a potential axial ligand for hemin. The β-sheet forming capability of the lysine-containing peptides is found to affect the catalytic synergy between the G-quadruplex DNA and the peptide. It is hypothesized that the β-sheet formation of the peptides results in the enrichment of the lysine residues, which distribute on the distal side of hemin to promote the formation of Compound I, like distal arginine residue in natural heme pocket. Incorporation of the histidine residues into the lysine-containing peptides further enhanced the hemin activities, indicating the cooperation between the lysine and histidine. Furthermore, the peptide/DNA/hemin complexes can be switched between active and inactive state by reversible formation and deformation of the DNA G-quadruplex, which was attributed to the peptides-promoted conformational changes of the DNA components. This work opens an avenue to mimic the catalytic residues and their spatial distribution in the natural enzymes, and shed light on the design of the smart biocatalysts that can respond to the environmental stimuli.
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Affiliation(s)
- Qiao Teng
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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11
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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12
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Jiao Y, Shang Y, Li N, Ding B. DNA-based enzymatic systems and their applications. iScience 2022; 25:104018. [PMID: 35313688 PMCID: PMC8933709 DOI: 10.1016/j.isci.2022.104018] [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] [Indexed: 11/06/2022] Open
Abstract
DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.
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13
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Yum JH, Sugiyama H, Park S. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives. CHEM REC 2022; 22:e202100333. [PMID: 35312235 DOI: 10.1002/tcr.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan.,Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan
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14
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Nakajima Y, Momotake A, Suzuki A, Neya S, Yamamoto Y. Nature of a H 2O Molecule Confined in the Hydrophobic Interface between the Heme and G-Quartet Planes in a Heme-DNA Complex. Biochemistry 2022; 61:523-534. [PMID: 35230084 DOI: 10.1021/acs.biochem.1c00751] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heme binds selectively to the 3'-terminal G-quartet of all parallel G-quadruplex DNAs to form stable heme-DNA complexes. Interestingly, the heme-DNA complexes exhibit various spectroscopic and functional properties similar to those of hemoproteins. Since the nature of the axial ligands is crucial in determining the physicochemical properties of heme, identification and characterization of the axial ligands in a heme-DNA complex are essential to elucidate the structure-function relationship in the complex. NMR studies of a complex possessing a low-spin ferric heme with a water molecule (H2O) and cyanide ion (CN-) as the axial ligands allowed detailed characterization of the physicochemical nature of the axial H2O ligand. We found that the in-plane asymmetry of the heme electronic structure of the complex is not largely affected by the axial H2O coordination, indicating that the H2O confined in the hydrophobic interface between the heme and G-quartet planes of the complex rotates about the coordination bond with respect to the heme. The effect of the hydrogen(H)/deuterium(D) isotope replacement of the axial H2O on the heme electronic structure was manifested in the isotope shifts of paramagnetically shifted heme methyl proton signals of the complex in such a manner that three resolved peaks associated with axial H2O, HDO, and D2O were observed for each of the heme methyl proton signals. These findings provide not only the basis for an understanding of the nature of the unique axial H2O but also an insight into the molecular mechanism responsible for the control of the heme reactivity in the heme-DNA complex.
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Affiliation(s)
- Yusuke Nakajima
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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15
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Li J, Wu H, Yan Y, Yuan T, Shu Y, Gao X, Zhang L, Li S, Ding S, Cheng W. Zippered G-quadruplex/hemin DNAzyme: exceptional catalyst for universal bioanalytical applications. Nucleic Acids Res 2021; 49:13031-13044. [PMID: 34878146 PMCID: PMC8682752 DOI: 10.1093/nar/gkab1178] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplex (G4)/hemin DNAzyme is promising horseradish peroxidase (HRP)-mimic candidate in the biological field. However, its relatively unsatisfactory catalytic capacity limits the potential applications. Inspired by nature protease, we conducted a proximity-enhanced cofactor assembly strategy (PECA) to form an exceptional HRP mimic, namely zippered G4/hemin DNAzyme (Z-G4/H). The hybridization of short oligonucleotides induced proximity assembly of the DNA-grafted hemin (DGH) with the complementary G4 sequences (cG4s), mimicking the tight configuration of protease cofactor and apoenzyme. The detailed investigations of catalytic efficiency and mechanism verified the higher activity, more rapid catalytic rate and high environmental tolerance of the Z-G4/H than the classical G4/hemin DNAzymes (C-G4/H). Furthermore, a proximity recognition transducer has been developed based on the PECA for sensitive detection of gene rearrangement and imaging human epidermal growth factor receptor 2 protein (HER2) dimerization on cell surfaces. Our studies demonstrate the high efficiency of Z-G4/H and its universal application potential in clinical diagnostics and biomolecule interaction research. It also may offer significant opportunities and inspiration for the engineering of the protease-free mimic enzyme.
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Affiliation(s)
- Jia Li
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Taixian Yuan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yue Shu
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xin Gao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lu Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Siqiao Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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16
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Araki H, Hagiwara S, Shinomiya R, Momotake A, Kotani H, Kojima T, Ochiai T, Shimada N, Maruyama A, Yamamoto Y. A cationic copolymer as a cocatalyst for a peroxidase-mimicking heme-DNAzyme. Biomater Sci 2021; 9:6142-6152. [PMID: 34346413 DOI: 10.1039/d1bm00949d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme binds to a parallel-stranded G-quadruplex DNA to form a peroxidase-mimicking heme-DNAzyme. An interpolyelectrolyte complex between the heme-DNAzyme and a cationic copolymer possessing protonated amino groups was characterized and the peroxidase activity of the complex was evaluated to elucidate the effect of the polymer on the catalytic activity of the heme-DNAzyme. We found that the catalytic activity of the heme-DNAzyme is enhanced through the formation of the interpolyelectrolyte complex due to the general acid catalysis of protonated amino groups of the polymer, enhancing the formation of the iron(iv)oxo porphyrin π-cation radical intermediate known as Compound I. This finding indicates that the polymer with protonated amino groups can act as a cocatalyst for the heme-DNAzyme in the oxidation catalysis. We also found that the enhancement of the activity of the heme-DNAzyme by the polymer depends on the local heme environment such as the negative charge density in the proximity of the heme and substrate accessibility to the heme. These findings provide novel insights as to molecular design of the heme-DNAzyme for enhancing its catalytic activity.
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Affiliation(s)
- Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takuro Ochiai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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17
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Hagiwara S, Momotake A, Ogura T, Yanagisawa S, Suzuki A, Neya S, Yamamoto Y. Effects of Heme Electronic Structure and Local Heme Environment on Catalytic Activity of a Peroxidase-Mimicking Heme-DNAzyme. Inorg Chem 2021; 60:11206-11213. [PMID: 34289695 DOI: 10.1021/acs.inorgchem.1c01179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic cycle of a peroxidase-mimicking heme-DNAzyme involves an iron(IV)oxo porphyrin π-cation radical intermediate known as compound I formed through heterolytic O-O bond cleavage of an Fe3+-bound hydroperoxo ligand (Fe-OOH) in compound 0, like that of a heme enzyme such as horseradish peroxidase (HRP). Peroxidase assaying of complexes composed of chemically modified hemes possessing various electron densities of the heme iron atom (ρFe) and parallel-stranded tetrameric G-quadruplex DNAs of oligonucleotides d(TTAGGG), d(TTAGGGT), and d(TTAGGGA) was performed to elucidate the effects of the heme electronic structure and local heme environment on the catalytic activity of the heme-DNAzyme. The study revealed that the DNAzyme activity is enhanced through an increase in the ρFe and general base catalysis of the adenine base adjacent to the heme, which are reminiscent of the "push" and "pull" mechanisms in the catalytic cycle of HRP, respectively, and that the activity of the heme-DNAzyme can be independently controlled through the heme electronic structure and local heme environment. These findings allow a deeper understanding of the structure-function relationship of the peroxidase-mimicking heme-DNAzyme.
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Affiliation(s)
- Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Akihiro Suzuki
- Department of Material Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan.,Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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18
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HO-1 and Heme: G-Quadruplex Interaction Choreograph DNA Damage Responses and Cancer Growth. Cells 2021; 10:cells10071801. [PMID: 34359970 PMCID: PMC8307061 DOI: 10.3390/cells10071801] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 02/04/2023] Open
Abstract
Many anti-cancer therapeutics lead to the release of danger associated pattern molecules (DAMPs) as the result of killing large numbers of both normal and transformed cells as well as lysis of red blood cells (RBC) (hemolysis). Labile heme originating from hemolysis acts as a DAMP while its breakdown products exert varying immunomodulatory effects. Labile heme is scavenged by hemopexin (Hx) and processed by heme oxygenase-1 (HO-1, Hmox1), resulting in its removal and the generation of biliverdin/bilirubin, carbon monoxide (CO) and iron. We recently demonstrated that labile heme accumulates in cancer cell nuclei in the tumor parenchyma of Hx knockout mice and contributes to the malignant phenotype of prostate cancer (PCa) cells and increased metastases. Additionally, this work identified Hx as a tumor suppressor gene. Direct interaction of heme with DNA G-quadruplexes (G4) leads to altered gene expression in cancer cells that regulate transcription, recombination and replication. Here, we provide new data supporting the nuclear role of HO-1 and heme in modulating DNA damage response, G4 stability and cancer growth. Finally, we discuss an alternative role of labile heme as a nuclear danger signal (NDS) that regulates gene expression and nuclear HO-1 regulated DNA damage responses stimulated by its interaction with G4.
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19
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Ma H, Wang L, Li Y, Wei Y. Guanosine-rich aptamers@Cu 2O nanoparticles: enhanced peroxidase activity and specific recognition capability at neutral pH. Chem Commun (Camb) 2021; 57:643-646. [PMID: 33346274 DOI: 10.1039/d0cc06877b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The decoration of Cu2O nanoparticles with guanosine-rich aptamers can significantly enhance their peroxidase activity at neutral pH and endow them with specific recognition capabilities. Both the phosphate backbone and guanine of the aptamers contribute to the enhancement. The excellent enzyme-like properties of this Cu2O-aptamer system make it a versatile platform for the development of neutral pH biosensors.
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Affiliation(s)
- Hongchao Ma
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Lan Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Yifan Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Yanhui Wei
- College of Chemistry and Material Science, Shandong Agricultural University, Taian, 271018, Shandong, P. R. China.
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20
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Canesin G, Di Ruscio A, Li M, Ummarino S, Hedblom A, Choudhury R, Krzyzanowska A, Csizmadia E, Palominos M, Stiehm A, Ebralidze A, Chen SY, Bassal MA, Zhao P, Tolosano E, Hurley L, Bjartell A, Tenen DG, Wegiel B. Scavenging of Labile Heme by Hemopexin Is a Key Checkpoint in Cancer Growth and Metastases. Cell Rep 2021; 32:108181. [PMID: 32966797 PMCID: PMC7551404 DOI: 10.1016/j.celrep.2020.108181] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/03/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022] Open
Abstract
Hemopexin (Hx) is a scavenger of labile heme. Herein, we present data defining the role of tumor stroma-expressed Hx in suppressing cancer progression. Labile heme and Hx levels are inversely correlated in the plasma of patients with prostate cancer (PCa). Further, low expression of Hx in PCa biopsies characterizes poorly differentiated tumors and correlates with earlier time to relapse. Significantly, heme promotes tumor growth and metastases in an orthotopic murine model of PCa, with the most aggressive phenotype detected in mice lacking Hx. Mechanistically, labile heme accumulates in the nucleus and modulates specific gene expression via interacting with guanine quadruplex (G4) DNA structures to promote PCa growth. We identify c-MYC as a heme:G4-regulated gene and a major player in heme-driven cancer progression. Collectively, these results reveal that sequestration of labile heme by Hx may block heme-driven tumor growth and metastases, suggesting a potential strategy to prevent and/or arrest cancer dissemination. Canesin et al. describe a role and mechanism for labile heme as a key player in regulating gene expression to promote carcinogenesis via binding to G-quadruplex in the c-MYC promoter. Hemopexin, a heme scavenger, may be used as a strategy to block progression of cancer.
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Affiliation(s)
- Giacomo Canesin
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Annalisa Di Ruscio
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA.
| | - Mailin Li
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy
| | - Simone Ummarino
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy
| | - Andreas Hedblom
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Reeham Choudhury
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Agnieszka Krzyzanowska
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Eva Csizmadia
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Macarena Palominos
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Anna Stiehm
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Alexander Ebralidze
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Shao-Yong Chen
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Mahmoud A Bassal
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA
| | - Ping Zhao
- College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Emanuela Tolosano
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Laurence Hurley
- College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Anders Bjartell
- Department of Translational Medicine, Division of Urological Cancers, Lund University, Malmo, Sweden
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, Singapore; Harvard Stem Cell Institute, Harvard Medical School, Cambridge, MA 02138, USA
| | - Barbara Wegiel
- Department of Surgery, Division of Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02214, USA.
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21
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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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22
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Okamoto C, Momotake A, Yamamoto Y. Structural and functional characterization of complexes between heme and dimeric parallel G-quadruplex DNAs. J Inorg Biochem 2021; 216:111336. [PMID: 33453496 DOI: 10.1016/j.jinorgbio.2020.111336] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Heme has been receiving considerable interest as a prosthetic group of ribozymes and deoxyribozymes, because heme-bound nucleic acids exhibit peroxidase-like catalytic activities (Travascio, P., Li, Y., and Sen, D. (1998) Chem. Biol, 5, 505-517). The interaction of heme with dimeric G-quadruplexes formed from d(TAGGGTTAGGGT) and d(TAGGGTTAGGGA) has been characterized to gain a deeper understanding of the molecular recognition of G-quadruplex DNAs by heme. We found that heme binds selectively to the 3'-terminal G-quartet of a dimeric parallel G-quadruplex of d(TAGGGTTAGGGT), whereas binding of heme to a dimeric antiparallel G-quadruplex of d(TAGGGTTAGGGA) does not occur, suggesting that an orderly arrangement of the constituent guanine deoxyribose rings, with respect to the G-quartet plane, is crucial for the binding of heme to the DNA. The preferential binding of heme to the 3'-terminal G-quartet of parallel G-quadruplex DNAs allowed a systematic modification of the heme environment in the complex through the DNA sequence. The activity of the complexes was found to increase with increasing number of adenine bases adjacent to the heme in the complexes, possibly due to improvement of the accessibility of aromatic substrate, i.e., 10-acetyl-3,7-dihydroxyphenoxazine, to the heme, and an increase in the frequency of appearance of a specific orientation of the adenine bases, with respect to the heme, optimized for its activity as an acid-base catalyst to enhance the peroxidase activity of the complex.
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Affiliation(s)
- China Okamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan; Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan.
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23
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Chambers IG, Willoughby MM, Hamza I, Reddi AR. One ring to bring them all and in the darkness bind them: The trafficking of heme without deliverers. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118881. [PMID: 33022276 PMCID: PMC7756907 DOI: 10.1016/j.bbamcr.2020.118881] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
Heme, as a hydrophobic iron-containing organic ring, is lipid soluble and can interact with biological membranes. The very same properties of heme that nature exploits to support life also renders heme potentially cytotoxic. In order to utilize heme, while also mitigating its toxicity, cells are challenged to tightly control the concentration and bioavailability of heme. On the bright side, it is reasonable to envision that, analogous to other transition metals, a combination of membrane-bound transporters, soluble carriers, and chaperones coordinate heme trafficking to subcellular compartments. However, given the dual properties exhibited by heme as a transition metal and lipid, it is compelling to consider the dark side: the potential role of non-proteinaceous biomolecules including lipids and nucleic acids that bind, sequester, and control heme trafficking and bioavailability. The emergence of inter-organellar membrane contact sites, as well as intracellular vesicles derived from various organelles, have raised the prospect that heme can be trafficked through hydrophobic channels. In this review, we aim to focus on heme delivery without deliverers - an alternate paradigm for the regulation of heme homeostasis through chaperone-less pathways for heme trafficking.
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Affiliation(s)
- Ian G Chambers
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20740, United States of America
| | - Mathilda M Willoughby
- School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, United States of America
| | - Iqbal Hamza
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20740, United States of America.
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, United States of America.
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24
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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25
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Mestre-Fos S, Ito C, Moore CM, Reddi AR, Williams LD. Human ribosomal G-quadruplexes regulate heme bioavailability. J Biol Chem 2020; 295:14855-14865. [PMID: 32817343 PMCID: PMC7606673 DOI: 10.1074/jbc.ra120.014332] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
The in vitro formation of stable G-quadruplexes (G4s) in human rRNA was recently reported. However, their formation in cells and their cellular roles were not resolved. Here, by taking a chemical biology approach that integrates results from immunofluorescence, G4 ligands, heme-affinity reagents, and a genetically encoded fluorescent heme sensor, we report that human ribosomes can form G4s in vivo that regulate heme bioavailability. Immunofluorescence experiments indicate that the vast majority of extra-nuclear G4s are associated with rRNA. Moreover, titrating human cells with a G4 ligand alters the ability of ribosomes to bind heme and disrupts cellular heme bioavailability as measured by a genetically encoded fluorescent heme sensor. Overall, these results suggest that ribosomes play a role in regulating heme homeostasis.
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Affiliation(s)
- Santi Mestre-Fos
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chieri Ito
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Courtney M Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Loren Dean Williams
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
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26
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Zhong H, Lo W, Man T, Williams BP, Li D, Chen S, Pei H, Li L, Tsung C. Stabilizing DNAzymes through Encapsulation in a Metal–Organic Framework. Chemistry 2020; 26:12931-12935. [DOI: 10.1002/chem.202002178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Huiye Zhong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Wei‐Shang Lo
- Department of Chemistry Merkert Chemistry Center Boston College 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Benjamin P. Williams
- Department of Chemistry Merkert Chemistry Center Boston College 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Sheng‐Yu Chen
- School of Physical Science and Technology ShanghaiTech University 393 Middle Huaxia Road Pudong, Shanghai 201210 P.R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Chia‐Kuang Tsung
- Department of Chemistry Merkert Chemistry Center Boston College 2609 Beacon Street Chestnut Hill MA 02467 USA
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27
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Cheng Y, Cheng M, Hao J, Jia G, Monchaud D, Li C. The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties. Chem Sci 2020; 11:8846-8853. [PMID: 34123138 PMCID: PMC8163442 DOI: 10.1039/d0sc02907f] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022] Open
Abstract
While many protein enzymes exert their functions through multimerization, which improves both selectivity and activity, this has not yet been demonstrated for other naturally occurring catalysts. Here, we report a multimerization effect applied to catalytic DNAs (or DNAzymes) and demonstrate that the enzymatic efficiency of G-quadruplexes (GQs) in interaction with the hemin cofactor is remarkably enhanced by homodimerization. The resulting non-covalent dimeric GQ-DNAzyme system provides hemin with a structurally defined active site in which both the cofactor (hemin) and the oxidant (H2O2) are activated. This new biocatalytic system efficiently performs peroxidase- and peroxygenase-type biotransformations of a broad range of substrates, thus providing new perspectives for biotechnological application of GQs.
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Affiliation(s)
- Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - David Monchaud
- Institut de Chimie Moléculaire de l' Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon 21078 Dijon France
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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28
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Lat PK, Liu K, Kumar DN, Wong KKL, Verheyen EM, Sen D. High specificity and tight spatial restriction of self-biotinylation by DNA and RNA G-Quadruplexes complexed in vitro and in vivo with Heme. Nucleic Acids Res 2020; 48:5254-5267. [PMID: 32329781 PMCID: PMC7261162 DOI: 10.1093/nar/gkaa281] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/24/2020] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Guanine-rich, single-stranded DNAs and RNAs that fold to G-quadruplexes (GQs) are able to complex tightly with heme and display strongly enhanced peroxidase activity. Phenolic compounds are particularly good substrates for these oxidative DNAzymes and ribozymes; we recently showed that the use of biotin-tyramide as substrate can lead to efficient GQ self-biotinylation. Such biotinylated GQs are amenable to polymerase chain reaction amplification and should be useful for a relatively non-perturbative investigation of GQs as well as GQ-heme complexes within living cells. Here, we report that in mixed solutions of GQ and duplex DNA in vitro, GQ biotinylation is specifically >104-fold that of the duplex, even in highly concentrated DNA gels; that a three-quartet GQ is tagged by up to four biotins, whose attachment occurs more or less uniformly along the GQ but doesn't extend significantly into a duplex appended to the GQ. This self-biotinylation can be modulated or even abolished in the presence of strong GQ ligands that compete with heme. Finally, we report strong evidence for the successful use of this methodology for labeling DNA and RNA within live, freshly dissected Drosophila larval salivary glands.
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Affiliation(s)
- Prince Kumar Lat
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kun Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dev N Kumar
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kenneth K L Wong
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Esther M Verheyen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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29
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Hayasaka K, Shibata T, Sugahara A, Momotake A, Matsui T, Neya S, Ishizuka T, Xu Y, Yamamoto Y. Characterization of Structure and Catalytic Activity of a Complex between Heme and an All Parallel-Stranded Tetrameric G-Quadruplex Formed from DNA/RNA Chimera Sequence d(TTA)r(GGG)dT. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kosuke Hayasaka
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Aya Sugahara
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Toru Matsui
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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30
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A compact nanobody-DNAzyme conjugate enables antigen detection and signal amplification. N Biotechnol 2020; 56:1-8. [DOI: 10.1016/j.nbt.2019.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022]
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31
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Wang J, Cheng M, Chen J, Ju H, Monchaud D, Mergny JL, Zhou J. An oxidatively damaged G-quadruplex/hemin DNAzyme. Chem Commun (Camb) 2020; 56:1839-1842. [PMID: 31950946 DOI: 10.1039/c9cc09237d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oxidative damage of guanine to 8-oxoguanine triggers a partial and variable loss of G-quadruplex/hemin DNAzyme activity and provides clues to the mechanistic origins of DNAzyme deactivation, which originates from an interplay between decreased G-quadruplex stability, lower hemin affinity and a modification of the nature of hemin binding sites.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - David Monchaud
- Institut de Chimie Moléculaire, Université de Bourgogne (ICMUB), CNRS UMR6302, UBFC Dijon 21000, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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32
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Hu L, Fu X, Kong G, Yin Y, Meng HM, Ke G, Zhang XB. DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging. J Mater Chem B 2020; 8:9449-9465. [DOI: 10.1039/d0tb01750g] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.
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Affiliation(s)
- Ling Hu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiaoyi Fu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Gezhi Kong
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Yao Yin
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Hong-Min Meng
- College of Chemistry
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiao-Bing Zhang
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
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33
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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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34
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Shinomiya R, Araki H, Momotake A, Kotani H, Kojima T, Yamamoto Y. Identification of Intermediates in Peroxidase Catalytic Cycle of a DNAzyme Possessing Heme. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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35
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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36
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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: 21] [Impact Index Per Article: 4.2] [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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37
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Wang Z, Li Y, Wang H, Wan K, Liu Q, Shi X, Ding B. Enzyme Mimic Based on a Self‐Assembled Chitosan/DNA Hybrid Exhibits Superior Activity and Tolerance. Chemistry 2019; 25:12576-12582. [DOI: 10.1002/chem.201902509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/15/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Zhen‐Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- State Key Laboratory of Organic-Inorganic CompositesBeijing University of Chemical Technology Beijing 100029 China
| | - Yunzhe Li
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Kaiwei Wan
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
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38
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Li W, Zeng W, Chen Y, Wang F, Wu F, Weng X, Zhou X. Biotinylation and isolation of an RNA G-quadruplex based on its peroxidase-mimicking activity. Analyst 2019; 144:4472-4476. [DOI: 10.1039/c9an00353c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The selective biotinylation of RNA G-quadruplexes can be used for pulling down RNA G-quadruplexes from an RNA mixture.
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Affiliation(s)
- Wei Li
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
| | - Weiwu Zeng
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
| | - Yi Chen
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071
- China
| | - Fan Wu
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
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39
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Yum JH, Park S, Sugiyama H. G-quadruplexes as versatile scaffolds for catalysis. Org Biomol Chem 2019; 17:9547-9561. [DOI: 10.1039/c9ob01876j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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40
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Kurapati R, Bianco A. Peroxidase mimicking DNAzymes degrade graphene oxide. NANOSCALE 2018; 10:19316-19321. [PMID: 30306169 DOI: 10.1039/c8nr06535g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNAzymes made of supramolecular guanine-rich G-quadruplexes and hemin are attracting a lot of interest due to their peroxidase activity mimicking the natural enzyme horseradish peroxidase (HRP). Herein, we demonstrate that DNAzyme consisting of a PS2.M-hemin complex can be an alternative to natural HRP for the oxidation and degradation of graphene oxide (GO). The degradation of GO sheets was carried out by incubating the PS2.M-hemin complex in the presence of hydrogen peroxide for 30 days. The degradation of GO has been confirmed using transmission electron microscopy and 2d Raman mapping. The current study suggests that the peroxidase activity of DNAzymes is similar to HRP and DNAzymes are able to degrade carbon-based nanomaterials.
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Affiliation(s)
- Rajendra Kurapati
- University of Strasbourg, CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, 67000 Strasbourg, France.
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41
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Chen J, Zhang Y, Cheng M, Guo Y, Šponer J, Monchaud D, Mergny JL, Ju H, Zhou J. How Proximal Nucleobases Regulate the Catalytic Activity of G-Quadruplex/Hemin DNAzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03811] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingying Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiri Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC Dijon 21078, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, 33600 Pessac, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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42
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Yamamoto Y, Araki H, Shinomiya R, Hayasaka K, Nakayama Y, Ochi K, Shibata T, Momotake A, Ohyama T, Hagihara M, Hemmi H. Structures and Catalytic Activities of Complexes between Heme and All Parallel-Stranded Monomeric G-Quadruplex DNAs. Biochemistry 2018; 57:5938-5948. [PMID: 30234971 DOI: 10.1021/acs.biochem.8b00792] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Heme in its ferrous and ferric states [heme(Fe2+) and heme(Fe3+), respectively] binds selectively to the 3'-terminal G-quartet of all parallel-stranded monomeric G-quadruplex DNAs formed from inosine(I)-containing sequences, i.e., d(TAGGGTGGGTTGGGTGIG) DNA(18mer) and d(TAGGGTGGGTTGGGTGIGA) DNA(18mer/A), through a π-π stacking interaction between the porphyrin moiety of the heme and the G-quartet, to form 1:1 complexes [heme-DNA(18mer) and heme-DNA(18mer/A) complexes, respectively]. These complexes exhibited enhanced peroxidase activities, compared with that of heme(Fe3+) alone, and the activity of the heme(Fe3+)-DNA(18mer/A) complex was greater than that of the heme(Fe3+)-DNA(18mer) one, indicating that the 3'-terminal A of the DNA sequence acts as an acid-base catalyst that promotes the catalytic reaction. In the complexes, a water molecule (H2O) at the interface between the heme and G-quartet is coordinated to the heme Fe atom as an axial ligand and possibly acts as an electron-donating ligand that promotes heterolytic peroxide bond cleavage of hydrogen peroxide bound to the heme Fe atom, trans to the H2O, for the generation of an active species. The intermolecular nuclear Overhauser effects observed among heme, DNA, and Fe-bound H2O indicated that the H2O rotates about the H2O-Fe coordination bond with respect to both the heme and DNA in the complex. Thus, the H2O in the complex is unique in terms of not only its electronic properties but also its dynamic ones. These findings provide novel insights into the design of heme-deoxyribozymes and -ribozymes.
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Affiliation(s)
- Yasuhiko Yamamoto
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan.,Tsukuba Research Center for Energy Materials Science (TREMS) , University of Tsukuba , Tsukuba 305-8571 , Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577 , Japan
| | - Haruka Araki
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Ryosuke Shinomiya
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Kosuke Hayasaka
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Yusaku Nakayama
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Kentaro Ochi
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Tomokazu Shibata
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Atsuya Momotake
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Takako Ohyama
- NMR Division, RIKEN SPring-8 Center , RIKEN , Suehiro-cho , Tsurumi-ku, Yokohama 230-0045 , Japan
| | - Masaki Hagihara
- Graduate School of Science and Technology , Hirosaki University , Hirosaki 036-8561 , Japan
| | - Hikaru Hemmi
- Food Research Institute , NARO , Tsukuba 305-8642 , Japan
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43
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Shinomiya R, Katahira Y, Araki H, Shibata T, Momotake A, Yanagisawa S, Ogura T, Suzuki A, Neya S, Yamamoto Y. Characterization of Catalytic Activities and Heme Coordination Structures of Heme-DNA Complexes Composed of Some Chemically Modified Hemes and an All Parallel-Stranded Tetrameric G-Quadruplex DNA Formed from d(TTAGGG). Biochemistry 2018; 57:5930-5937. [PMID: 30207701 DOI: 10.1021/acs.biochem.8b00793] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Heme binds selectively to the 3'-terminal G-quartet (G6 G-quartet) of an all parallel-stranded tetrameric G-quadruplex DNA, [d(TTAGGG)]4, to form a heme-DNA complex. Complexes between [d(TTAGGG)]4 and a series of chemically modified hemes possessing a heme Fe atom with a variety of electron densities were characterized in terms of their peroxidase activities to evaluate the effect of a change in the electron density of the heme Fe atom (ρFe) on their activities. The peroxidase activity of a complex decreased with a decreasing ρFe, supporting the idea that the activity of the complex is elicited through a reaction mechanism similar to that of a peroxidase. In the ferrous heme-DNA complex, carbon monoxide (CO) can bind to the heme Fe atom on the side of the heme opposite the G6 G-quartet, and a water molecule (H2O) is coordinated to the Fe atom as another axial ligand, trans to the CO. The stretching frequencies of Fe-bound CO (νCO) and the Fe-C bond (νFe-C) of CO adducts of the heme-DNA complexes were determined to investigate the structural and electronic natures of the axial ligands coordinated to the heme Fe atom. Comparison of the νCO and νFe-C values of the heme-DNA complexes with those of myoglobin (Mb) revealed that the donor strength of the axial ligation trans to the CO in a complex is considerably weaker than that of the proximal histidine in Mb, as expected from the coordination of H2O trans to the CO in the complex.
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Affiliation(s)
- Ryosuke Shinomiya
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Yuya Katahira
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Haruka Araki
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Tomokazu Shibata
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Atsuya Momotake
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science , University of Hyogo , Hyogo 678-1297 , Japan
| | - Takashi Ogura
- Graduate School of Life Science , University of Hyogo , Hyogo 678-1297 , Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology , Nagaoka College , Nagaoka 940-8532 , Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences , Chiba University , Chuoh-Inohana , Chiba 260-8675 , Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan.,Tsukuba Research Center for Energy Materials Science (TREMS) , University of Tsukuba , Tsukuba 305-8571 , Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA) , University of Tsukuba , Tsukuba 305-8577 , Japan
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44
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Hemschemeier A, Happe T. The plasticity of redox cofactors: from metalloenzymes to redox-active DNA. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0029-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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45
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Wang ZG, Wang H, Liu Q, Duan F, Shi X, Ding B. Designed Self-Assembly of Peptides with G-Quadruplex/Hemin DNAzyme into Nanofibrils Possessing Enzyme-Mimicking Active Sites and Catalytic Functions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00896] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Fangyuan Duan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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46
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Vitas M, Dobovišek A. In the Beginning was a Mutualism - On the Origin of Translation. ORIGINS LIFE EVOL B 2018; 48:223-243. [PMID: 29713988 DOI: 10.1007/s11084-018-9557-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/23/2018] [Indexed: 12/28/2022]
Abstract
The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.
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Affiliation(s)
- Marko Vitas
- , Laze pri Borovnici 38, Borovnica, Slovenia.
| | - Andrej Dobovišek
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia
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47
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Ai T, Yang Q, Lv Y, Huang Y, Li Y, Geng J, Xiao D, Zhou C. Insight into How Telomeric G-Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin. Chem Asian J 2018; 13:1805-1810. [PMID: 29718585 DOI: 10.1002/asia.201800464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/30/2018] [Indexed: 02/05/2023]
Abstract
The toxic oxidative damage of G-quadruplexes (G4), linked to neurodegenerative diseases, may arise from their ability to bind and oxidatively activate cellular hemin. However, there have been no precise studies on how telomeric G4 enhances the low intrinsic peroxidase activity of hemin. Herein, a label-free and nanopore-based strategy was developed to explore the enhancement mechanism of peroxidase activity of hemin induced by telomeric G4 (d(TTAGGG)n ). The nanopore-based strategy demonstrated that there were simultaneously two different binding modes of telomere G4 to hemin. At the single-molecule level, it was found that the hybrid structural telomeric G4 directly binds to hemin (the affinity constant (Ka )≈106 m-1 ) to form a tight complex, and some of them underwent a topological change to a parallel structure with an enhancement of Ka to approximately 107 m-1 . Through detailed analysis of the topology and peroxidase activity and molecular modeling investigations, the parallel telomere G4/hemin DNAzyme structure was proven to be preferable for high peroxidase activity. Upon strong π-π stacking, the parallel structural telomere G4 supplied a key axial ligand to the hemin iron, which accelerated the intermediate compound formation with H2 O2 in the catalytic cycle. Our studies developed a label-free and single-molecule strategy to fundamentally understand the catalytic activity and mechanism of telomeric DNAzyme, which provides some support for utilizing the toxic, oxidative-damage property in cellular oxidative disease and anticancer therapeutics.
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Affiliation(s)
- Tingting Ai
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Qiufang Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - You Lv
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuqin Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuzhi Li
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Jia Geng
- Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P.R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
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48
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Wang Y, Shan D, Wu G, Wang H, Ru F, Zhang X, Li L, Qian Y, Lu X. A novel “dual-potential” ratiometric electrochemiluminescence DNA sensor based on enhancing and quenching effect by G-quadruplex / hemin and Au-Luminol bifunctional nanoparticles. Biosens Bioelectron 2018; 106:64-70. [DOI: 10.1016/j.bios.2018.01.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 11/26/2022]
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49
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He C, Zheng S, Zhang J, Li W, Fu Y. Hunting for the “Sweet Spot”: Effects of Contiguous Guanines and Strand Lengths on the Catalytic Performance of DNA-Based Peroxidase Mimetics. Catal Letters 2018. [DOI: 10.1007/s10562-018-2356-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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50
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Xu J, Guo J, Maina SW, Yang Y, Hu Y, Li X, Qiu J, Xin Z. An aptasensor for staphylococcus aureus based on nicking enzyme amplification reaction and rolling circle amplification. Anal Biochem 2018; 549:136-142. [PMID: 29550346 DOI: 10.1016/j.ab.2018.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 12/21/2022]
Abstract
An ultra-sensitive aptamer-based biosensor for the detection of staphylococcus aureus was established by adopting the nicking enzyme amplification reaction (NEAR) and the rolling circle amplification (RCA) technologies. Aptamer-probe (AP), containing an aptamer and a probe sequence, was developed to act as the recognition unit of the biosensor, which was specifically bound to S. aureus. The probe was released from AP and initiated into the subsequent DNA amplification reactions where S. aureus was present, converting the detection of S. aureus to the investigation of probe oligonucleotide. The RCA amplification products contained a G-quadruplex motif and formed a three dimensional structure in presence of hemin. The G4/hemin complex showed horseradish peroxidase (HRP)-mimic activity and catalyzed the chemiluminescence reaction of luminol mediated by H2O2. The results showed that the established biosensor could detect S. aureus specifically with a good linear correlation at 5-104 CFU/mL. The signal values based on NEAR-RCA two-step cycle were boosted acutely, much higher than that relied on one-cycle magnification. The limit of detection (LoD) was determined to be as low as 5 CFU/mL. The established aptasensor exhibited a good discrimination of living against dead S. aureus, and can be applied to detect S. aureus in the food industry.
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Affiliation(s)
- Jingguo Xu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jia Guo
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Sarah Wanjiku Maina
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yumeng Yang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yimin Hu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xuanxuan Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jiarong Qiu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China.
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