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Fujita S, Sugio Y, Kawamura T, Yamagami R, Oka N, Hirata A, Yokogawa T, Hori H. ArcS from Thermococcus kodakarensis transfers L-lysine to preQ 0 nucleoside derivatives as minimum substrate RNAs. J Biol Chem 2024; 300:107505. [PMID: 38944122 PMCID: PMC11298593 DOI: 10.1016/j.jbc.2024.107505] [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: 02/01/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
Archaeosine (G+) is an archaea-specific tRNA modification synthesized via multiple steps. In the first step, archaeosine tRNA guanine transglucosylase (ArcTGT) exchanges the G15 base in tRNA with 7-cyano-7-deazaguanine (preQ0). In Euryarchaea, preQ015 in tRNA is further modified by archaeosine synthase (ArcS). Thermococcus kodakarensis ArcS catalyzes a lysine-transfer reaction to produce preQ0-lysine (preQ0-Lys) as an intermediate. The resulting preQ0-Lys15 in tRNA is converted to G+15 by a radical S-adenosyl-L-methionine enzyme for archaeosine formation (RaSEA), which forms a complex with ArcS. Here, we focus on the substrate tRNA recognition mechanism of ArcS. Kinetic parameters of ArcS for lysine and tRNA-preQ0 were determined using a purified enzyme. RNA fragments containing preQ0 were prepared from Saccharomyces cerevisiae tRNAPhe-preQ015. ArcS transferred 14C-labeled lysine to RNA fragments. Furthermore, ArcS transferred lysine to preQ0 nucleoside and preQ0 nucleoside 5'-monophosphate. Thus, the L-shaped structure and the sequence of tRNA are not essential for the lysine-transfer reaction by ArcS. However, the presence of D-arm structure accelerates the lysine-transfer reaction. Because ArcTGT from thermophilic archaea recognizes the common D-arm structure, we expected the combination of T. kodakarensis ArcTGT and ArcS and RaSEA complex would result in the formation of preQ0-Lys15 in all tRNAs. This hypothesis was confirmed using 46 T. kodakarensis tRNA transcripts and three Haloferax volcanii tRNA transcripts. In addition, ArcTGT did not exchange the preQ0-Lys15 in tRNA with guanine or preQ0 base, showing that formation of tRNA-preQ0-Lys by ArcS plays a role in preventing the reverse reaction in G+ biosynthesis.
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Affiliation(s)
- Shu Fujita
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Yuzuru Sugio
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Natsuhisa Oka
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Gifu, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Gifu, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
| | - Akira Hirata
- Department of Natural Science, Graduate School of Technology, Industrial and Social Science, Tokushima University, Tokushima, Tokushima, Japan
| | - Takashi Yokogawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Gifu, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
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Iwata T, Kurahashi Y, Wijaya IMM, Kandori H. Spectroscopic Investigation of Na +-Dependent Conformational Changes of a Cyclobutane Pyrimidine Dimer-Repairing Deoxyribozyme. ACS OMEGA 2023; 8:37274-37281. [PMID: 37841180 PMCID: PMC10569015 DOI: 10.1021/acsomega.3c05083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
UV1C is an enzymatically active DNA sequence (deoxyribozyme, DNAzyme) that functions as a cyclobutane pyrimidine dimer (CPD) photolyase. UV1C forms parallel guanine quadruplexes (G-quadruplexes) with a DNA substrate in the presence of 240 mM Na+, the structure of which is important for the enzymatic activity. To investigate the repair mechanism of CPD by UV1C, we designed light-induced Fourier transform infrared (FTIR) spectroscopy. Prior to FTIR measurements, circular dichroism (CD) spectroscopy was conducted to determine the Na+ concentration at which the most G-quadruplexes were formed. We found that UV1C also forms a hybrid G-quadruplex structure at over 500 mM Na+. By assuming a concentration equilibrium between G-quadruplexes and Na+, 1.3 and 1.8 Na+ were found to bind to parallel and hybrid G-quadruplexes, respectively. The hybrid G-quadruplex form of UV1C was also suggested to exhibit photolyase activity. Light-induced FTIR spectra recorded upon the photorepair of CPD by UV1C were compared for parallel G-quadruplex-rich and hybrid G-quadruplex-rich samples. Spectral variations were indicative of structural differences in parallel and hybrid G-quadruplexes before and after CPD cleavage. Differences were also observed when compared to the CPD repair spectrum by CPD photolyase. The spectral differences during CPD repair by either protein or DNAzyme suggest the local environment of the substrates, the surrounding protein, or the aqueous solution.
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Affiliation(s)
- Tatsuya Iwata
- Department
of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yuhi Kurahashi
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - I Made Mahaputra Wijaya
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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3
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Calabria D, Zangheri M, Pour SRS, Trozzi I, Pace A, Lazzarini E, Calabretta MM, Mirasoli M, Guardigli M. Luminescent Aptamer-Based Bioassays for Sensitive Detection of Food Allergens. BIOSENSORS 2022; 12:644. [PMID: 36005040 PMCID: PMC9405952 DOI: 10.3390/bios12080644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/06/2023]
Abstract
The presence of hidden allergens in food products, often due to unintended contamination along the food supply chain (production, transformation, processing, and transport), has raised the urgent need for rapid and reliable analytical methods for detecting trace levels of such species in food products. Indeed, food allergens represent a high-risk factor for allergic subjects due to potentially life-threatening adverse reactions. Portable biosensors based on immunoassays have already been developed as rapid, sensitive, selective, and low-cost analytical platforms that can replace analyses with traditional bench-top instrumentation. Recently, aptamers have attracted great interest as alternative biorecognition molecules for bioassays, since they can bind a variety of targets with high specificity and selectivity, and they enable the development of assays exploiting a variety of transduction and detection technologies. In particular, aptasensors based on luminescence detection have been proposed, taking advantage of the development of ultrasensitive tracers and enhancers. This review aims to summarize and discuss recent efforts in the field of food allergen analysis using aptamer-based bioassays with luminescence detection.
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Affiliation(s)
- Donato Calabria
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
| | - Martina Zangheri
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Agrofood Research (CIRI AGRO), Alma Mater Studiorum, University of Bologna, Via Quinto Bucci 336, I-47521 Cesena, Italy
- Interdepartmental Centre for Industrial Research in Advanced Mechanical Engineering Applications and Materials Technology (CIRI MAM), Alma Mater Studiorum, University of Bologna, Viale Risorgimento 2, I-40136 Bologna, Italy
| | - Seyedeh Rojin Shariati Pour
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Ilaria Trozzi
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Andrea Pace
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Elisa Lazzarini
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Maria Maddalena Calabretta
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Mara Mirasoli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
| | - Massimo Guardigli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
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4
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Sanford AA, Manuel BA, Romero-Reyes MA, Heemstra JM. Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids. Chem Sci 2022; 13:7670-7684. [PMID: 35865900 PMCID: PMC9258336 DOI: 10.1039/d2sc00117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Brea A Manuel
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Misael A Romero-Reyes
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Chemistry, Hanover College Hanover Indiana 47243 USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta GA 30332 USA
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5
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Liu C, Gou S, Bi Y, Gao Q, Sun J, Hu S, Guo W. Smart DNA-gold nanoparticle hybrid hydrogel film based portable, cost-effective and storable biosensing system for the colorimetric detection of lead (II) and uranyl ions. Biosens Bioelectron 2022; 210:114290. [PMID: 35489275 DOI: 10.1016/j.bios.2022.114290] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022]
Abstract
A portable, cost-effective and storable DNA-gold nanoparticle (AuNP) hybrid hydrogel film based biosensing system was developed, with AuNPs serving as both the crosslinking units of the film and the signaling units. Using a layer-by-layer assembly method, hydrogel film composed of three-dimensional hydrophilic network of densely packed AuNPs interconnected by responsive DNA structures was constructed onto a glass slide. By programming the sequence of DNA structures, target-responsive hybrid films were constructed. As a proof of concept, the sequence of a substrate DNA which can be identified and cleaved by Pb2+-dependent DNAzyme was encoded to construct Pb2+-responsive DNA-AuNP hybrid hydrogel film. The high-density packing of AuNPs as signal substances significantly improved the sensitivity of the ultrathin film biosensing system while reduced the cost of expensive DNA materials. A hydrogel film composed of 10 layers of assembled DNA-AuNP structures generated sufficient visual colorimetric signals for Pb2+ detection, with a detection limit of 2.6 nM. By introducing UO22+-dependent DNAzyme, the system could be further applied in the sensitive and selective detection of UO22+, with a detection limit of 10.3 nM. Compared with bulk-sized DNA hydrogel biosensing systems, the DNA-AuNP hydrogel film biosensing system exhibited faster response thanks to the sub-micrometer ultrathin film structures. Moreover, the protection of fragile non-covalently crosslinked DNA films with solid slides also facilitated the portable application and long-term storage of the resulting biosensing system, with 95% of the response signal retained after three months of storage. The DNA-AuNPs hydrogel film biosensing system is highly promising for future rapid on-site detection applications.
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Affiliation(s)
- Chang Liu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Siyu Gou
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Yanhui Bi
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Qi Gao
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Juanjuan Sun
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Shanjin Hu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China
| | - Weiwei Guo
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
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6
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Liaqat A, Sednev MV, Höbartner C. In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications. Methods Mol Biol 2022; 2533:167-179. [PMID: 35796988 PMCID: PMC9761555 DOI: 10.1007/978-1-0716-2501-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N 6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.
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Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Maksim V Sednev
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany.
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8
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Arakawa S, Kamizaki K, Kuwana Y, Kataoka N, Naoe C, Takemoto C, Yokogawa T, Hori H. Application of solid-phase DNA probe method with cleavage by deoxyribozyme for analysis of long non-coding RNAs. J Biochem 2020; 168:273-283. [PMID: 32289169 DOI: 10.1093/jb/mvaa048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/02/2020] [Indexed: 11/12/2022] Open
Abstract
The solid-phase DNA probe method is a well-established technique for tRNA purification. We have applied this method for purification and analysis of other non-coding RNAs. Three columns for purification of tRNAPhe, transfer-messenger RNA (tmRNA) and 16S rRNA from Thermus thermophilus were connected in tandem and purifications were performed. From each column, tRNAPhe, tmRNA and 16S rRNA could be purified in a single step. This is the first report of purification of native tmRNA from T. thermophilus and the purification demonstrates that the solid-phase DNA probe method is applicable to non-coding RNA, which is present in lower amounts than tRNA. Furthermore, if a long non-coding RNA is cleaved site-specifically and the fragment can be purified by the solid-phase DNA probe method, modified nucleosides in the long non-coding RNA can be analysed. Therefore, we designed a deoxyribozyme (DNAzyme) to perform site-specific cleavage of 16S rRNA, examined optimum conditions and purified the resulting RNA fragment. Sequencing of complimentary DNA and mass spectrometric analysis revealed that the purified RNA corresponded to the targeted fragment of 16S rRNA. Thus, the combination of DNAzyme cleavage and purification using solid-phase DNA probe methodology can be a useful technique for analysis of modified nucleosides in long non-coding RNAs.
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Affiliation(s)
- Shizuka Arakawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kohsuke Kamizaki
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yusuke Kuwana
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Naruki Kataoka
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Chieko Naoe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chie Takemoto
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Yokogawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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Debiais M, Lelievre A, Smietana M, Müller S. Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors. Nucleic Acids Res 2020; 48:3400-3422. [PMID: 32112111 PMCID: PMC7144939 DOI: 10.1093/nar/gkaa132] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Amandine Lelievre
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
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DMLR: A toolkit for investigation of deoxyribozyme-mediated ligation based on real time PCR. Biochem Biophys Res Commun 2020; 524:405-410. [PMID: 32007270 DOI: 10.1016/j.bbrc.2020.01.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 11/21/2022]
Abstract
Deoxyribozymes or DNAzyme are identified as catalytic DNA sequences which catalyze different chemical reactions. Ligating deoxyribozymes catalyze the formation of branched and linear products. Due to the lack of efficient read-out systems, there is no report on in vivo application of ligating deoxyribozymes. To expand the biological application of branched-RNA forming deoxyribozymes, we performed our study in order to suggest a practical toolkit for measurement of in vivo real-time activity of ligating deoxyribozymes. Further in vitro studies were designed to analyze the effects of the location of branch site on reverse transcriptase (RT) interference. With this toolkit even the activity of RT was measured precisely. Our results indicate that the activity of RT enzyme significantly affected by a 17 nt branched adaptor synthesized by 10DM24 ligating deoxyribozyme. The RT stalls at or near the RNA branch point during both initiation and elongation phases. The DNA synthesis is decreased 4.3 and 2.7 fold during initiation and elongation phases respectively. In conclusion, we introduce a general and practical toolkit called "DMLR" which is based on Real-time PCR method. The use of DMLR precisely determines RT behavior when encountered with any backbone modification with the ability of stopping the enzyme activity.
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Kuhlmann A, Hermann S, Weinberger M, Penner A, Wagenknecht HA. Photocatalysis with nucleic acids and peptides. PHYSICAL SCIENCES REVIEWS 2018. [DOI: 10.1515/psr-2017-0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In chemical photocatalysis, the photophysical process is coupled to a subsequent chemical reaction. The absorbed light energy contributes to the overall energy balance of the reaction and thereby increases its sustainability. Additionally, oligonucleotides and oligopeptides offer the possibility to control regio- and stereoselectivity as catalysts of organic reactions by providing potential substrate binding sites. We follow this path and want to explore how important substrate binding sites are for photocatalysis. The general concepts of photochemistry and biooligomer catalysis are combined for photochemically active DNAzymes for [2 + 2]-cycloadditions and proline-rich short peptides for nucleophilic additions to styrenes.
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12
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Marek JJ, Hennecke U. Why DNA Is a More Effective Scaffold than RNA in Nucleic Acid-Based Asymmetric Catalysis-Supramolecular Control of Cooperative Effects. Chemistry 2017; 23:6009-6013. [DOI: 10.1002/chem.201606043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Jasmin J. Marek
- Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Correnstraße 40 48149 Münster Germany
| | - Ulrich Hennecke
- Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Correnstraße 40 48149 Münster Germany
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Wang S, Liu C, Li G, Sheng Y, Sun Y, Rui H, Zhang J, Xu J, Jiang D. The Triple Roles of Glutathione for a DNA-Cleaving DNAzyme and Development of a Fluorescent Glutathione/Cu 2+-Dependent DNAzyme Sensor for Detection of Cu 2+ in Drinking Water. ACS Sens 2017; 2:364-370. [PMID: 28723208 DOI: 10.1021/acssensors.6b00667] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pistol-like DNAzyme (PLDz) is an oxidative DNA-cleaving catalytic DNA with ascorbic acid as cofactor. Herein, glutathione was induced into the reaction system to maintain reduced ascorbic acid levels for higher efficient cleavage. However, data indicated that glutathione played triple roles in PLDz-catalyzed reactions. Glutathione alone had no effect on PLDz, and showed inhibitory effect on ascorbic acid-induced PLDz catalysis, but exhibited stimulating effect on Cu2+-promoted self-cleavage of PLDz. Further analysis of the effect of glutathione/Cu2+ on PLDz indicated that H2O2 played a key role in PLDz catalysis. Finally, we developed a fluorescent Cu2+ sensor (PL-Cu 1.0) based on the relationship between glutathione/Cu2+ and catalytic activity of PLDz. The fluorescent intensity showed a linear response toward the logarithm concentration of Cu2+ over the range from 80 nM to 30 μM, with a detection limit of 21.1 nM. PL-Cu 1.0 provided only detection of Cu2+ over other divalent metal ions. Ca2+ and Mg2+ could not interfere with Cu2+ detection even at a 1000-fold concentration. We further applied PL-Cu 1.0 for Cu2+ detection in tap and bottled water. Water stored in copper taps overnight had relatively high Cu2+ concentrations, with a maximum 22.3 μM. Trace Cu2+ (52.2 nM) in deep spring was detected among the tested bottled water. Therefore, PL-Cu 1.0 is feasible to detect Cu2+ in drinking water, with a practical application.
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Affiliation(s)
- Shijin Wang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Chengcheng Liu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Guiying Li
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Yongjie Sheng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Yanhong Sun
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Hongyue Rui
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Jin Zhang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
| | - Jiacui Xu
- College
of Animal Sciences, Jilin University, 5333# Xi’an Road, Changchun 130062, China
| | - Dazhi Jiang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China
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14
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Marek JJ, Singh RP, Heuer A, Hennecke U. Enantioselective Catalysis by Using Short, Structurally Defined DNA Hairpins as Scaffold for Hybrid Catalysts. Chemistry 2017; 23:6004-6008. [PMID: 28029714 DOI: 10.1002/chem.201606002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 11/09/2022]
Abstract
A new type of DNA metal complex hybrid catalyst, which is based on single-stranded DNA oligonucleotides, is described. It was shown that oligonucleotides as short as 14 nucleotides that fold into hairpin structures are suitable as nucleic acid components for DNA hybrid catalysts. With these catalysts, excellent enantioinduction in asymmetric Diels-Alder reactions with selectivity values as high as 96 % enantiomeric excess (ee) can be achieved. Molecular dynamics simulations indicate that a rather flexible loop combined with a rigid stem region provides DNA scaffolds with these high selectivity values.
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Affiliation(s)
- Jasmin J Marek
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstrasse 40, 48149, Münster, Germany
| | - Raghvendra P Singh
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Andreas Heuer
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Ulrich Hennecke
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstrasse 40, 48149, Münster, Germany
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15
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Zhao Z, Lin F, Ye H, Huang R, Xu X. Effects of modified-guanosine on the stability of G-triplex. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.10.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Liu C, Sheng Y, Sun Y, Feng J, Wang S, Zhang J, Xu J, Jiang D. A glucose oxidase-coupled DNAzyme sensor for glucose detection in tears and saliva. Biosens Bioelectron 2015; 70:455-61. [PMID: 25863343 DOI: 10.1016/j.bios.2015.03.070] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/15/2015] [Accepted: 03/27/2015] [Indexed: 02/05/2023]
Abstract
Biosensors have been widely investigated and utilized in a variety of fields ranging from environmental monitoring to clinical diagnostics. Glucose biosensors have triggered great interest and have been widely exploited since glucose determination is essential for diabetes diagnosis. In here, we designed a novel dual-enzyme biosensor composed of glucose oxidase (GOx) and pistol-like DNAzyme (PLDz) to detect glucose levels in tears and saliva. First, GOx, as a molecular recognition element, catalyzes the oxidation of glucose forming H2O2; then PLDz recognizes the produced H2O2 as a secondary signal and performs a self-cleavage reaction promoted by Mn(2+), Co(2+) and Cu(2+). Thus, detection of glucose could be realized by monitoring the cleavage rate of PLDz. The slope of the cleavage rate of PLDz versus glucose concentration curve was fitted with a Double Boltzmann equation, with a range of glucose from 100 nM to 10mM and a detection limit of 5 μM. We further applied the GOx-PLDz 1.0 biosensor for glucose detection in tears and saliva, glucose levels in which are 720±81 μM and 405±56 μM respectively. Therefore, the GOx-PLDz 1.0 biosensor is able to determine glucose levels in tears and saliva as a noninvasive glucose biosensor, which is important for diabetic patients with frequent/continuous glucose monitoring requirements. In addition, induction of DNAzyme provides a new approach in the development of glucose biosensors.
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Affiliation(s)
- Chengcheng Liu
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yongjie Sheng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yanhong Sun
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Junkui Feng
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Shijin Wang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Jin Zhang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China.
| | - Jiacui Xu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
| | - Dazhi Jiang
- Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Qianjin Street 2699, Changchun 130012, China.
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17
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Zhao H. DNA Stability in Ionic Liquids and Deep Eutectic Solvents. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2015; 90:19-25. [PMID: 31929671 PMCID: PMC6953985 DOI: 10.1002/jctb.4511] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA molecules are known as the genetic information carriers. Recently, they are being explored as a new generation of biocatalysts or chiral scaffolds for metal catalysts. There is also a growing interest of finding alternative solvents for DNA preservation and stabilization, including two unique types of solvents: ionic liquids (ILs) and deep eutectic solvents (DES). Therefore, it is important to understand how DNA molecules interact with these novel ionic solvent systems (i.e. ILs and DES). It is well known that inorganic di- and monovalent ions preferentially bind with major and minor grooves of DNA structures. However, in the case of ILs and DES, organic cation may intrude into the DNA minor grooves; more importantly, electrostatic attraction between organic cations and the DNA phosphate backbone becomes a predominant interaction, accompanying by hydrophobic and polar interactions between ILs and DNA major and minor grooves. In addition, anions may form hydrogen-bonds with cytosine, adenine and guanine bases. Despites these strong interactions, DNA molecules maintain double helical structure in most ionic solvent systems, especially in aqueous IL solutions. Furthermore, the exciting advances of G-quadruplexe DNA structures in ILs and DES are discussed.
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Affiliation(s)
- Hua Zhao
- Department of Chemistry and Forensic Science, Savannah State University, Savannah, GA 31404, USA
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18
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Kanezaki H, Nishimoto SI, Tanabe K. Regulation of DNAzyme function by hypoxic irradiation that induces one-electron reduction of 2-oxoalkyl group on thymine base. ACTA ACUST UNITED AC 2014. [DOI: 10.5857/rcp.2014.3.4.79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Tanabe K, Okada K, Sugiura M, Ito T, Nishimoto SI. Hypoxic X-irradiation as an external stimulus for conformational change of oligodeoxynucleotides that possess disulfide bond and regulation of DNAzyme function. Bioorg Med Chem Lett 2014; 25:310-2. [PMID: 25479773 DOI: 10.1016/j.bmcl.2014.11.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 12/17/2022]
Abstract
We achieved a conformational change of oligodeoxynucleotides and the regulation of DNAzyme function by means of a radiolytic strand exchange reaction of disulfide bond. We designed a system in which the DNAzyme function of RNA cleavage was suppressed by the hybridization of an inhibitor strand that possessed disulfide bond with an active DNAzyme. Hypoxic X-irradiation led to the recovery of RNA cleavage because the strand exchange reaction at the disulfide bond in inhibitor strand resulted in a release of inhibitor strand. This strategy may be applicable to gene regulation by hypoxic X-irradiation.
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Affiliation(s)
- Kazuhito Tanabe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Kana Okada
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masaaki Sugiura
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sei-Ichi Nishimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
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20
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Wang G, Chen L, Zhu Y, He X, Xu G, Zhang X. Development of an electrochemical sensor based on the catalysis of ferrocene actuated hemin/G-quadruplex enzyme for the detection of potassium ions. Biosens Bioelectron 2014; 61:410-6. [DOI: 10.1016/j.bios.2014.05.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
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21
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DNA from natural sources in design of functional devices. Methods 2014; 67:105-15. [DOI: 10.1016/j.ymeth.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 01/01/2023] Open
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22
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Kondo J, Yamada T, Hirose C, Okamoto I, Tanaka Y, Ono A. Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs. Angew Chem Int Ed Engl 2014; 53:2385-8. [PMID: 24478025 DOI: 10.1002/anie.201309066] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/06/2013] [Indexed: 11/09/2022]
Abstract
The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo (Japan).
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23
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Kondo J, Yamada T, Hirose C, Okamoto I, Tanaka Y, Ono A. Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-HgII-T Base Pairs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309066] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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24
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Deoxyribozyme-Mediated Ligation for Incorporating EPR Spin Labels and Reporter Groups into RNA. Methods Enzymol 2014; 549:85-104. [DOI: 10.1016/b978-0-12-801122-5.00004-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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25
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Abstract
Recently, DNA has been evaluated as a chiral scaffold for metal complexes to construct so called 'DNA-based hybrid catalysts', a robust and inexpensive alternative to enzymes. The unique chiral structure of DNA allows the hybrid catalysts to catalyze various asymmetric synthesis reactions. However, most current studies used aqueous buffers as solvents for these asymmetric reactions, where substrates/products are typically suspended in the solutions. The mass transfer limitation usually requires a long reaction time. To overcome this hurdle and to advance DNA-based asymmetric catalysis, we evaluated a series of ionic liquids (ILs), inorganic salts, deep eutectic solvents (DES), glymes, glycols, acetonitrile and methanol as co-solvents/additives for the DNA-based asymmetric Michael addition. In general, these additives induce indistinguishable changes to the DNA B-form duplex conformation as suggested by circular dichroism (CD) spectroscopy, but impose a significant influence on the catalytic efficiency of the DNA-based hybrid catalyst. Conventional organic solvents (e.g. acetonitrile and methanol) led to poor product yields and/or low enantioselectivities. Most ILs and inorganic salts cause the deactivation of the hybrid catalyst except 0.2 M [BMIM][CF3COO] (95.4% ee and 93% yield) and 0.2 M [BMIM]Cl (93.7% ee and 89% yield). Several other additives have also been found to improve the catalytic efficiency of the DNA-based hybrid catalyst (control reaction without additive gives >99% ee and 87% yield): 0.4 M glycerol (>99% ee and 96% yield at 5 °C or 96.2% ee and 83% yield at room temperature), 0.2 M choline chloride/glycerol (1:2) (92.4% ee and 90% yield at 5 °C or 94.0% ee and 88% yield at room temperature), and 0.5 M dipropylene glycol dimethyl ether (>99% ee and 87% yield at room temperature). The use of some co-solvents/additives allows the Michael addition to be performed at a higher temperature (e.g. room temperature vs 5 °C) and a shorter reaction time (24 h vs 3 days). In addition, we found that a brief pre-sonication (5 min) of DNA in MOPS buffer prior to the reaction could improve the performance of the DNA-based hybrid catalyst. We have also shown that this DNA-based catalysis method is suitable for a variety of different substrates and relatively large-scale reactions. In conclusion, a judicious selection of benign co-solvents/additives could improve the catalytic efficiency of DNA-based hybrid catalyst.
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Affiliation(s)
- Hua Zhao
- Department of Chemistry and Forensic Science, Savannah State University, Savannah, GA 31404, USA
| | - Kai Shen
- Department of Chemistry and Forensic Science, Savannah State University, Savannah, GA 31404, USA
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26
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Seio K, Kanamori T, Tokugawa M, Ohzeki H, Masaki Y, Tsunoda H, Ohkubo A, Sekine M. Fluorescent properties of oligonucleotides doubly modified with an indole-fused cytosine analog and 2-aminopurine. Bioorg Med Chem 2013; 21:3197-201. [PMID: 23628471 DOI: 10.1016/j.bmc.2013.03.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 11/16/2022]
Abstract
Single- and double-stranded oligodeoxynucleotides (ODNs) incorporating both 2-aminopurine (2AP) and an indole-fused cytosine analog (PPI) were prepared and studied for their fluorescence properties. PPI and 2AP can be excited simultaneously by irradiation at 300 nm, with emission observed at 500 nm for PPI and 370 nm for 2AP. We demonstrated the utility of these properties in the dual fluorescence labeling of ODNs giving well-separated emission peaks. In addition, both of the fluorescence signals of a doubly modified ODN changed independently, reflecting the local duplex formation at the regions containing 2AP or PPI. Potential applications of this strategy for the dual fluorescence labeling of oligonucleotides with 2AP and PPI include monitoring local structure alterations of functional nucleic acids and the multiplex detection of biologically important nucleic acids.
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Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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27
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Wang S, Fu B, Peng S, Zhang X, Tian T, Zhou X. The G-triplex DNA could function as a new variety of DNA peroxidase. Chem Commun (Camb) 2013; 49:7920-2. [DOI: 10.1039/c3cc44075c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Xiang Y, Wu P, Tan LH, Lu Y. DNAzyme-functionalized gold nanoparticles for biosensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:93-120. [PMID: 24026635 DOI: 10.1007/10_2013_242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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29
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Pyrazole-bridged late first row transition metal complexes derived from hexadentate compartmental ligand: synthesis, characterization, antibacterial activity, and DNA binding/cleavage studies. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0199-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Jung J, Han KY, Koh HR, Lee J, Choi YM, Kim C, Kim SK. Effect of Single-Base Mutation on Activity and Folding of 10-23 Deoxyribozyme Studied by Three-Color Single-Molecule ALEX FRET. J Phys Chem B 2012; 116:3007-12. [DOI: 10.1021/jp2117196] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiwon Jung
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Kyu Young Han
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Hye Ran Koh
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Jihyun Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Yoon Mi Choi
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Christine Kim
- Columbia University Medical Center, New York, New York 10032, United States
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
- WCU Department of Biophysics and
Chemical Biology, Seoul National University, Seoul 151-747, Korea
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31
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Single-stranded DNAzyme-based Pb2+ fluorescent sensor that can work well over a wide temperature range. Biosens Bioelectron 2012; 34:159-64. [PMID: 22370100 DOI: 10.1016/j.bios.2012.01.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/27/2012] [Accepted: 01/27/2012] [Indexed: 10/14/2022]
Abstract
DNAzymes have become an excellent choice for sensing applications. Based on DNAzymes, three generations of Pb(2+) fluorescent sensors have been reported. In these sensors, two oligonucleotide strands (substrate strand and enzyme strand) were used, which not only increased the complexity of the detection system, but also brought some difficulties for the use of the sensors at elevated temperatures. To overcome this problem, a single-stranded DNAzyme-based Pb(2+) fluorescent sensor was designed by combining the substrate sequence and the enzyme sequence into one oligonucleotide strand. The intramolecular duplex structure of this single-stranded DNAzyme kept the fluorophore and the quencher, labeled at its two ends, in close proximity; thus the background fluorescence was significantly suppressed. Using this fluorescent sensor, Pb(2+) quantitation can be achieved with high sensitivity and high selectivity. In addition, the extraordinary stability of the intramolecular duplex structure could assure a low background fluorescence at high temperature, even if the number of complementary base pairs between the substrate sequence and the enzyme sequence was reduced, allowing the sensor to work well over a wide temperature range. Similar performances of the fluorescent sensor at 4, 25 and 37°C suggested that this sensor has a good ability to resist temperature fluctuations.
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32
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Graber D, Trappl K, Steger J, Geiermann AS, Rigger L, Moroder H, Polacek N, Micura R. Deoxyribozyme-based, semisynthetic access to stable peptidyl-tRNAs exemplified by tRNAVal carrying a macrolide antibiotic resistance peptide. Methods Mol Biol 2012; 848:201-213. [PMID: 22315071 DOI: 10.1007/978-1-61779-545-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a protocol for the reliable synthesis of non-hydrolyzable 3'-peptidyl-tRNAs that contain all the respective genuine nucleoside modifications. The approach is exemplified by tRNA(Val)-3'-NH-VFLVM-NH(2) and relies on commercially available Escherichia coli tRNA(Val). This tRNA was cleaved site-specifically within the TΨC loop using a 10-23 type DNA enzyme to obtain a 58 nt tRNA 5'-fragment which contained the modifications. After cleavage of the 2',3'-cyclophosphate moiety from the 5'-fragment, it was ligated to the 18 nt RNA-pentapeptide conjugate which had been chemically synthesized. By this methodology, tRNA(Val)-3'-NH-VFLVM-NH(2) is accessible in efficient manner. Furthermore, we point out that the approach is applicable to other types of tRNA.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Base Sequence
- DNA, Catalytic/metabolism
- Drug Resistance, Bacterial
- Escherichia coli
- Macrolides/pharmacology
- Mass Spectrometry
- Models, Molecular
- Nucleic Acid Conformation
- Peptides
- Phenol/chemistry
- Phosphorylation
- RNA Stability
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemical synthesis
- RNA, Transfer, Val/chemical synthesis
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/isolation & purification
- RNA, Transfer, Val/metabolism
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Affiliation(s)
- Dagmar Graber
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innsbruck, Austria
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33
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Abstract
The discovery of DNAzymes that can catalyze a wide range of reactions in the presence of metal ions is important on both fundamental and practical levels; it advances our understanding of metal-nucleic acid interactions and allows for the design of highly sensitive and selective metal ion sensors. A crucial factor in this success is a technique known as in vitro selection, which can rapidly select metal-specific RNA-cleaving DNAzymes. In vitro selection is an iterative process where a DNA pool containing a random region is incubated with the target metal ion. Those DNA sequences that catalyze the preferred reaction (the "winners") are amplified and carried on to the next step, where the selection is carried out under more stringent conditions. In this way, the selection pool becomes enriched with DNAzymes that exhibit desirable activity and selectivity. The method described can be applied to isolate DNAzymes selective to many different types of metal ions or different oxidation states of the same metal ion.
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34
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Zheng AX, Li J, Wang JR, Song XR, Chen GN, Yang HH. Enzyme-free signal amplification in the DNAzyme sensor via target-catalyzed hairpin assembly. Chem Commun (Camb) 2012; 48:3112-4. [DOI: 10.1039/c2cc30305a] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Lan T, Lu Y. Metal Ion-Dependent DNAzymes and Their Applications as Biosensors. Met Ions Life Sci 2012; 10:217-48. [DOI: 10.1007/978-94-007-2172-2_8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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36
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Sen D, Poon LCH. RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean? Crit Rev Biochem Mol Biol 2011; 46:478-92. [PMID: 21958168 DOI: 10.3109/10409238.2011.618220] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Guanine-rich RNAs and DNAs from chromosomal telomeres and elsewhere that fold into guanine quadruplexes (G-quadruplexes), are found to complex tightly with porphyrins such as N-methylmesoporphyrin IX (NMM) and hemin [Fe(III) heme]. By themselves, these DNAs and RNAs are found to be efficient catalysts for porphyrin metallation. When complexed with hemin, under physiological conditions, these nucleic acids display robust peroxidase (one-electron oxidation), as well as peroxygenase (two-electron oxidation, or oxygen transfer) activity. These surprising catalytic properties, that frequently match the catalytic performance of natural peroxidase and P450 monooxygenase enzymes, have been the subject of significant mechanistic analysis, as well as having found utility in a wide range of biosensing and other applications. This review summarizes recent insights into a surprising yet fundamental property of many RNAs and DNAs, a property with undoubted ramifications for cellular oxidative disease, de novo hemoenzyme design, and our understanding of the evolution of early biocatalytic systems.
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Affiliation(s)
- Dipankar Sen
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
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Liu X, Freeman R, Golub E, Willner I. Chemiluminescence and chemiluminescence resonance energy transfer (CRET) aptamer sensors using catalytic hemin/G-quadruplexes. ACS NANO 2011; 5:7648-7655. [PMID: 21866963 DOI: 10.1021/nn202799d] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The incorporation of hemin into the thrombin/G-quadruplex aptamer assembly or into the ATP/G-quadruplex nanostructure yields active DNAzymes that catalyze the generation of chemiluminescence. These catalytic processes enable the detection of thrombin and ATP with detection limits corresponding to 200 pM and 10 μM, respectively. The conjugation of the antithrombin or anti-ATP aptamers to CdSe/ZnS semiconductor quantum dots (QDs) allowed the detection of thrombin or ATP through the luminescence of the QDs that is powered by a chemiluminescence resonance energy-transfer (CRET) process stimulated by the hemin/G-quadruplex/thrombin complex or the hemin/G-quadruplex/ATP nanostructure, in the presence of luminol/H(2)O(2). The advantages of applying the CRET process for the detection of thrombin or ATP, by the resulting hemin/G-quadruplex DNAzyme structures, are reflected by low background signals and the possibility to develop multiplexed aptasensor assays using different sized QDs.
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Affiliation(s)
- Xiaoqing Liu
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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38
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Kosman J, Juskowiak B. Peroxidase-mimicking DNAzymes for biosensing applications: a review. Anal Chim Acta 2011; 707:7-17. [PMID: 22027115 DOI: 10.1016/j.aca.2011.08.050] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 08/23/2011] [Accepted: 08/29/2011] [Indexed: 12/11/2022]
Abstract
DNAzymes are single stranded DNA molecules that exhibit catalytic activity and are exploited in medicine, biology and material sciences. Development in this area is related to the many advantages of DNAzymes over conventional protein enzymes, such as thermal stability and simpler preparation. DNAzymes with peroxidase-like activity have recently attracted great interest. To assure such catalytic activity, oligonucleotides have to adopt a G-quadruplex structure, which can bind the hemin molecule. This system facilitates a redox reaction between the target molecule and hydrogen peroxide, which results in the appearance of an oxidized target molecule (product). DNAzymes with peroxidase-mimicking activity have great potential in bioanalytical chemistry. This review presents fundamentals concerning the design and engineering of DNAzymes with peroxidase-like activity, describes their properties and spectral characteristics and shows how DNAzymes can contribute to bioanalytical research. Examples of bioanalytical applications of DNAzymes with peroxidase-like activity include nucleic acid probes with DNAzyme labels for the detection of specific DNA sequences in colorimetric or chemiluminescent assays. Assays for telomerase or methyltransferase activity, which are potential targets in anticancer therapy, are also described in this review. Other applications include the determination of metal cations such as Ag(+), K(+), Hg(2+), Pb(2+) or Cu(2+) and amplified detection of small molecules such as adenosine, cocaine or AMP and proteins such as lysozyme or thrombin. In the last decade, DNAzymes have become part of numerous applications in many areas of science from chemistry to biology to medicine.
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Affiliation(s)
- Joanna Kosman
- Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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39
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Won BY, Shin S, Fu R, Shin SC, Cho DY, Park HG. A one-step electrochemical method for DNA detection that utilizes a peroxidase-mimicking DNAzyme amplified through PCR of target DNA. Biosens Bioelectron 2011; 30:73-7. [PMID: 21940158 DOI: 10.1016/j.bios.2011.08.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/09/2011] [Accepted: 08/23/2011] [Indexed: 11/26/2022]
Abstract
A novel one-step electrochemical method for DNA detection is described. The procedure utilizes a reaction catalyzed by a peroxidase-mimicking DNAzyme to produce a product, which forms an insoluble precipitation layer on the surface of an electrode. A rationally designed forward primer, conjugated with a peroxidase DNAzyme complementary sequence at its 5'-end, is used for PCR amplification of target DNA. As a result, the DNAzyme sequence is produced by amplification only when the target DNA is present in the sample. The PCR product is then subjected to the precipitation reaction on the electrode surface using an electrolyte assay buffer containing 4-chloronaphthol, hydrogen peroxide, ferrocenemethanol, hemin, and 5'-lambdaexonuclease. Finally, analysis is carried out using Faradaic impedance spectroscopy. The impedance value was found to greatly increase when target DNA is present owing to the formation of a precipitation layer on the electrode surface caused by the catalytic action of the DNAzyme. In contrast, no impedance increase is observed when a control sample not containing target DNA is utilized. By employing this strategy, target DNA from Chlamydia trachomatis was reliably detected within a 10 min period following precipitation without the need for complicated secondary procedures. This effort has led to the development of a highly convenient electrochemical one-step method for DNA detection that utilizes a peroxidase-mimicking DNAzyme, which is specifically designed to undergo amplification during PCR of target DNA.
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Affiliation(s)
- Byoung Yeon Won
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, Daejeon 305-701, Republic of Korea
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40
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Wachowius F, Javadi-Zarnaghi F, Höbartner C. Combinatorial mutation interference analysis reveals functional nucleotides required for DNA catalysis. Angew Chem Int Ed Engl 2011; 49:8504-8. [PMID: 20872387 DOI: 10.1002/anie.201003940] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Falk Wachowius
- Research group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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41
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Poon LCH, Methot SP, Morabi-Pazooki W, Pio F, Bennet AJ, Sen D. Guanine-rich RNAs and DNAs that bind heme robustly catalyze oxygen transfer reactions. J Am Chem Soc 2011; 133:1877-84. [PMID: 21265562 DOI: 10.1021/ja108571a] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diverse guanine-rich RNAs and DNAs that fold to form guanine quadruplexes are known to form tight complexes with Fe(III) heme. We show here that a wide variety of such complexes robustly catalyze two-electron oxidations, transferring oxygen from hydrogen peroxide to thioanisole, indole, and styrene substrates. Use of (18)O-labeled hydrogen peroxide reveals the source of the oxygen transferred to form thioanisole sulfoxide and styrene oxide to be the activated ferryl moiety within these systems. Hammett analysis of the kinetics of thioanisole sulfoxide formation is unable to distinguish between a one-step, direct oxygen transfer and a two-step, oxygen rebound mechanism for this catalysis. Oxygen transfer to indole produces a range of products, including indigo and related dyes. Docking of heme onto a high-resolution structure of the G-quadruplex fold of Bcl-2 promoter DNA, which both binds heme and transfers oxygen, suggests a relatively open active site for this class of ribozymes and deoxyribozymes. That heme-dependent catalysis of oxygen transfer is a property of many RNAs and DNAs has ramifications for primordial evolution, enzyme design, cellular oxidative disease, and anticancer therapeutics.
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Affiliation(s)
- Lester C-H Poon
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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42
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Functional Nucleic Acids for Fluorescence-Based Biosensing Applications. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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43
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Wachowius F, Javadi-Zarnaghi F, Höbartner C. Kombinatorische Mutationsinterferenz-Analyse zur Untersuchung funktioneller Nucleotide in Desoxyribozymen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003940] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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44
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Young DD, Lively MO, Deiters A. Activation and deactivation of DNAzyme and antisense function with light for the photochemical regulation of gene expression in mammalian cells. J Am Chem Soc 2010; 132:6183-93. [PMID: 20392038 DOI: 10.1021/ja100710j] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The photochemical regulation of biological systems represents a very precise means of achieving high-resolution control over gene expression in both a spatial and a temporal fashion. DNAzymes are enzymatically active deoxyoligonucleotides that enable the site-specific cleavage of RNA and have been used in a variety of in vitro applications. We have previously reported the photochemical activation of DNAzymes and antisense agents through the preparation of a caged DNA phosphoramidite and its site-specific incorporation into oligonucleotides. The presence of the caging group disrupts either DNA:RNA hybridization or catalytic activity until removed via a brief irradiation with UV light. Here, we are expanding this concept by investigating the photochemical deactivation of DNAzymes and antisense agents. Moreover, we report the application of light-activated and light-deactivated antisense agents to the regulation of gene function in mammalian cells. This represents the first example of gene silencing antisense agents that can be turned on and turned off in mammalian tissue culture.
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Affiliation(s)
- Douglas D Young
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Jiang D, Xu J, Sheng Y, Sun Y, Zhang J. An allosteric DNAzyme with dual RNA-cleaving and DNA-cleaving activities. FEBS J 2010; 277:2543-9. [PMID: 20553490 DOI: 10.1111/j.1742-4658.2010.07669.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of RNA-cleaving or DNA-cleaving DNAzymes have been obtained by in vitro selection. However, engineering an allosteric DNAzyme with dual RNA-cleaving and DNA-cleaving activities is very challenging. We used an in vitro-selected pistol-like (PL) DNAzyme as a DNA scaffold for designing a DNAzyme with dual catalytic activities. We prepared the 46-nucleotide DNAzyme with DNA-cleaving activity (PL DNAzyme), and then grafted the deoxyribonucleotide residues from an 8-17 variant DNAzyme into the region of stem-loop I and the catalytic core of the PL DNAzyme scaffold. This deoxyribonucleotide residue grafting resulted in a DNAzyme with dual RNA-cleaving and DNA-cleaving activities (DRc DNAzyme). Drc DNAzyme has properties different from those of the original PL DNAzyme, including DNA cleavage sites and the required metal ion concentration. Interestingly, the RNA substrate and RNase A can act as effectors to mediate the DNA cleavage. Our results show that RNA-cleaving and DNA-cleaving activities simultaneously coexist in DRc DNAzyme, and the DNA cleavage activity can be reversibly regulated by a conformational transition.
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Affiliation(s)
- Dazhi Jiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, China
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46
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Budagumpi S, Revankar VK. Interaction of E. coli DNA with diazine-bridged late first row transition metal complexes derived from hexadentate compartmental ligands: an approach to DNA cleavage/binding studies. TRANSIT METAL CHEM 2010. [DOI: 10.1007/s11243-010-9376-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Graber D, Moroder H, Steger J, Trappl K, Polacek N, Micura R. Reliable semi-synthesis of hydrolysis-resistant 3'-peptidyl-tRNA conjugates containing genuine tRNA modifications. Nucleic Acids Res 2010; 38:6796-802. [PMID: 20525967 PMCID: PMC2965236 DOI: 10.1093/nar/gkq508] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The 3′-peptidyl-tRNA conjugates that possess a hydrolysis-resistant ribose-3′-amide linkage instead of the natural ester linkage would represent valuable substrates for ribosomal studies. Up to date, access to these derivatives is severely limited. Here, we present a novel approach for the reliable synthesis of non-hydrolyzable 3′-peptidyl-tRNAs that contain all the respective genuine nucleoside modifications. In short, the approach is based on tRNAs from natural sources that are site-specifically cleaved within the TΨC loop by using DNA enzymes to obtain defined tRNA 5′-fragments carrying the modifications. After dephosphorylation of the 2′,3′-cyclophosphate moieties from these fragments, they are ligated to the respective 3′-peptidylamino-tRNA termini that were prepared following the lines of a recently reported solid-phase synthesis. By this novel concept, non-hydrolyzable 3′-peptidyl-tRNA conjugates possessing all natural nucleoside modifications are accessible in highly efficient manner.
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Affiliation(s)
- Dagmar Graber
- Institute of Organic Chemistry, Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
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48
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Kenward M, Dorfman KD. Coarse-Grained Brownian Dynamics Simulations of the 10-23 DNAzyme. Biophys J 2010; 97:2785-93. [PMID: 19917233 DOI: 10.1016/j.bpj.2009.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/01/2009] [Accepted: 09/02/2009] [Indexed: 11/18/2022] Open
Abstract
Deoxyribozymes (DNAzymes) are single-stranded DNA that catalyze nucleic acid biochemistry. Although a number of DNAzymes have been discovered by in vitro selection, the relationship between their tertiary structure and function remains unknown. We focus here on the well-studied 10-23 DNAzyme, which cleaves mRNA with a catalytic efficiency approaching that of RNase A. Using coarse-grained Brownian dynamics simulations, we find that the DNAzyme bends its substrate away from the cleavage point, exposing the reactive site and buckling the DNAzyme catalytic core. This hypothesized transition state provides microscopic insights into experimental observations concerning the size of the DNAzyme/substrate complex, the impact of the recognition arm length, and the sensitivity of the enzymatic activity to point mutations of the catalytic core. Upon cleaving the pertinent backbone bond in the substrate, we find that the catalytic core of the DNAzyme unwinds and the overall complex rapidly extends, in agreement with experiments on the related 8-17 DNAzyme. The results presented here provide a starting point for interpreting experimental data on DNAzyme kinetics, as well as developing more detailed simulation models. The results also demonstrate the limitations of using a simple physical model to understand the role of point mutations.
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Affiliation(s)
- Martin Kenward
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
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49
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Lu K, Miyazaki Y, Summers MF. Isotope labeling strategies for NMR studies of RNA. JOURNAL OF BIOMOLECULAR NMR 2010; 46:113-25. [PMID: 19789981 PMCID: PMC2797625 DOI: 10.1007/s10858-009-9375-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/20/2009] [Indexed: 05/04/2023]
Abstract
The known biological functions of RNA have expanded in recent years and now include gene regulation, maintenance of sub-cellular structure, and catalysis, in addition to propagation of genetic information. As for proteins, RNA function is tightly correlated with structure. Unlike proteins, structural information for larger, biologically functional RNAs is relatively limited. NMR signal degeneracy, relaxation problems, and a paucity of long-range (1)H-(1)H dipolar contacts have limited the utility of traditional NMR approaches. Selective isotope labeling, including nucleotide-specific and segmental labeling strategies, may provide the best opportunities for obtaining structural information by NMR. Here we review methods that have been developed for preparing and purifying isotopically labeled RNAs, as well as NMR strategies that have been employed for signal assignment and structure determination.
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Affiliation(s)
- Kun Lu
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Yasuyuki Miyazaki
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Michael F. Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
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50
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Smuga D, Majchrzak K, Sochacka E, Nawrot B. RNA-cleaving 10–23 deoxyribozyme with a single amino acid-like functionality operates without metal ion cofactors. NEW J CHEM 2010. [DOI: 10.1039/b9nj00705a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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