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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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2
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Anbalagan S. Temperature-sensing riboceptors. RNA Biol 2024; 21:1-6. [PMID: 39016038 PMCID: PMC11259075 DOI: 10.1080/15476286.2024.2379118] [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] [Revised: 06/19/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
Understanding how cells sense temperature is a fundamental question in biology and is pivotal for the evolution of life. In numerous organisms, temperature is not only sensed but also generated due to cellular processes. Consequently, the mechanisms governing temperature sensation in various organisms have been experimentally elucidated. Extending upon others' proposals and demonstration of protein- and nucleic acid-based thermosensors, and utilizing a colonial India 'punkah-wallahs' analogy, I present my rationale for the necessity of temperature sensing in every organelle in a cell. Finally, I propose temperature-sensing riboceptors (ribonucleic acid receptors) to integrate all the RNA molecules (mRNA, non-coding RNA, and so forth) capable of sensing temperature and triggering a signaling event, which I call as thermocrine signaling. This approach could enable the identification of riboceptors in every cell of almost every organism, not only for temperature but also for other classes of ligands, including gaseous solutes, and water.
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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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3
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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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4
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Yang G, Li W, Zhang S, Hu B, Huang Z. Highly-efficient selection of aptamers for detecting various HPV subtypes in clinical samples. Talanta 2024; 266:125039. [PMID: 37604070 DOI: 10.1016/j.talanta.2023.125039] [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: 06/10/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023]
Abstract
Nucleic acid aptamers are of great potentials in diagnostic and therapeutic applications because of their unique molecular recognition capabilities. However, satisfactory aptamers with high affinity and specificity are still in short supply. Herein, we have developed new selection methods allowing the free interactions between the targets and potential aptamers in solution. In our selection system, the protein targets (biotinylated randomly or site-specifically) were first incubated with the random DNA library, followed by the pull-down with the streptavidin magnetic beads or biolayer-interferometry (BLI) sensors. By comparing the two biotinylation strategies (random or site-specific) and two states of the targets (free or immobilized), we have found that the combination of the site-specific biotinylation and free-target strategies was most successful. Based on these highly-efficient selection strategies, HPV L1 aptamers were obtained. By designing the sandwich aptasensor assisted with RCA and CRISPR/Cas12a, we have diagnosed various HPV subtypes in clinical samples, such as easily-collected urine samples. In summary, our new strategy can allow efficient selection of aptamers with high affinity and specificity for clinical applications.
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Affiliation(s)
- Guotai Yang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Wei Li
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610000, PR China; SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, 610095, PR China.
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5
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Wang Z, Shi W, Tan Y, Liu B. A homogeneous label-free electrochemical aptasensor based on an omega-like DNA nanostructure for progesterone detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6159-6164. [PMID: 37955623 DOI: 10.1039/d3ay01255g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
A novel homogeneous label-free electrochemical aptamer sensor for the detection of progesterone was prepared by combining a well-designed omega (Ω)-like DNA (Ω-DNA) nanostructure, with an isothermal cycling amplification strategy based on the highly efficient exonuclease III (Exo III). The omega-like (Ω) DNA is composed of two oligonucleotide strands: DNA1 and DNA2. The Pro aptamer triggers a chain displacement reaction of Ω-DNA nanostructures, forms a new double-stranded DNA structure (aptamer precursor-DNA2), and releases DNA1. Then, Exo III selectively cleaves the DNA duplex and releases the Pro aptamer to participate in a new displacement reaction. Meanwhile, the released DNA1 strands gain access to the strongly bound hemin, forming a hemin/G-quadruplex (DNAzyme). In the presence of hydrogen peroxide (H2O2), differential pulse voltammetry (DPV) was used to detect the current signal from the oxidation of o-phenylenediamine (OPD) to aminoazobenzene (DAP) catalyzed by DNAzyme. However, the amount of released DNA1 from the Ω-DNA nanostructures is reduced in the presence of the target Pro, and the DPV signal declines because of the small amount of DNAzyme formed. The developed electrochemical aptasensor has a wide dynamic linear relationship in the range of 1 pg mL-1 to 10 ng mL-1 under optimal conditions. Its detection limit is down to 0.3 pg mL-1, providing a potential platform for a sensitive Pro assay among electrochemical assays.
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Affiliation(s)
- Zaofen Wang
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
| | - Weiping Shi
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
| | - Yunzhu Tan
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
| | - Bingqian Liu
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
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Cvjetan N, Schuler LD, Ishikawa T, Walde P. Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate. ACS OMEGA 2023; 8:42878-42899. [PMID: 38024761 PMCID: PMC10652838 DOI: 10.1021/acsomega.3c05915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3',5,5'-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.
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Affiliation(s)
- Nemanja Cvjetan
- Department
of Materials, ETH-Zürich, Leopold-Ruzicka-Weg 4, 8093 Zürich, Switzerland
| | | | - Takashi Ishikawa
- Department
of Biology and Chemistry, Paul Scherrer Institute and Department of
Biology, ETH-Zürich, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Peter Walde
- Department
of Materials, ETH-Zürich, Leopold-Ruzicka-Weg 4, 8093 Zürich, Switzerland
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7
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Wu M, Yang B, Shi L, Tang Q, Wang J, Liu W, Li B, Jin Y. Peroxidase-Mimicking DNAzymes as Receptors for Label-Free Discriminating Heavy Metal Ions by Chemiluminescence Sensor Arrays. Anal Chem 2023; 95:3486-3492. [PMID: 36733985 DOI: 10.1021/acs.analchem.2c05447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Receptors are crucial to the analytical performance of sensor arrays. Different from the previous receptors in sensor arrays, herein, peroxidase-mimicking DNAzymes were innovatively used as receptors to develop a label-free chemiluminescence sensor array for discriminating various heavy metal ions in complex samples. The peroxidase-mimicking DNAzymes are composed of functional oligonucleotides and hemin, including G-triplex-hemin DNAzyme (G3-DNAzyme), G-quadruplex-hemin DNAzyme (G4-DNAzyme), and the dimer of G-quadruplex-hemin DNAzyme (dG4-DNAzyme). Circular dichroism (CD) spectroscopy demonstrated that different metal ions diversely affect the conformation of G-quadruplex and G-triplex, resulting in a change in the activity of peroxidase-mimicking DNAzyme. Thus, the unique fingerprints formed to easily discriminate seven kinds of heavy metal ions by principal component analysis (PCA) within 20 min. The discrimination of unknown metal ions in tap water further confirmed its ability for discriminating multiple heavy metal ions. Moreover, it will not bring water pollution due to the good biocompatibility of DNA. Therefore, it not only merely offers a label-free, rapid, environment-friendly, and cheap (1.49 $) sensor assay for discriminating metal ions but also comes up with an innovative way for developing sensor arrays.
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Affiliation(s)
- Mengmeng Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bing Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Qiaorong Tang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wei Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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8
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Biver T. Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules. Molecules 2022; 27:molecules27134165. [PMID: 35807410 PMCID: PMC9268745 DOI: 10.3390/molecules27134165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered.
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Affiliation(s)
- Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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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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10
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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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11
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Okamoto C, Momotake A, Kobayashi M, Yamamoto Y. Molecular recognition of G-quadruplex DNA by Pheophorbide a. CHEM LETT 2021. [DOI: 10.1246/cl.210130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
| | - Masami Kobayashi
- Department of Materials Science, 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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