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Volek M, Kurfürst J, Drexler M, Svoboda M, Srb P, Veverka V, Curtis E. Aurora: a fluorescent deoxyribozyme for high-throughput screening. Nucleic Acids Res 2024; 52:9049-9061. [PMID: 38860424 PMCID: PMC11347150 DOI: 10.1093/nar/gkae467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Fluorescence facilitates the detection, visualization, and tracking of molecules with high sensitivity and specificity. A functional DNA molecule that generates a robust fluorescent signal would offer significant advantages for many applications compared to intrinsically fluorescent proteins, which are expensive and labor intensive to synthesize, and fluorescent RNA aptamers, which are unstable under most conditions. Here, we describe a novel deoxyriboyzme that rapidly and efficiently generates a stable fluorescent product using a readily available coumarin substrate. An engineered version can detect picomolar concentrations of ribonucleases in a simple homogenous assay, and was used to rapidly identify novel inhibitors of the SARS-CoV-2 ribonuclease Nsp15 in a high-throughput screen. Our work adds an important new component to the toolkit of functional DNA parts, and also demonstrates how catalytic DNA motifs can be used to solve real-world problems.
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Affiliation(s)
- Martin Volek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Jaroslav Kurfürst
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Matúš Drexler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Michal Svoboda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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2
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Xie X, Cheng X, Dong J, Li J, Jiang L, Yang T, Liao B, Ding S, Liu Q, Luo F, Cheng W, Chen J. Visual Assay for Methicillin-Resistant Staphylococcus aureus Based on Rolling Circular Amplification Triggering G-Quadruplex/Hemin DNAzyme Proximity Assembly. Anal Chem 2023; 95:3098-3107. [PMID: 36693787 DOI: 10.1021/acs.analchem.2c05712] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nowadays, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have constituted a new challenge for anti-infective treatment. Precise identification and rapid clinical diagnostics of MRSA from other methicillin-sensitive strains entail assays with robust diagnostic efficiency and simple operation steps. Sensitive detection of MecA gene is promising to indicate MRSA infection, but it is challenged by the lack of isothermal and simple strategies. A visual assay based on isothermal rolling circular amplification and G-quadruplex/hemin (G4/hemin) DNAzyme proximity assembly was proposed for the immediate, efficient, and cost-effective detection of MecA in simple operation steps and in a single tube. The presence of MecA specifically drove the formation of circular templates, which further triggered isothermal amplification. The amplified product offered abundant binding sites for DNA-grafted hemin probes to form a novel proximity-assembled G4/hemin DNAzyme structure for colorimetric changing diagnosis. This tandem-repeated novel DNAzyme possessed higher catalytic activity and a lower background signal than traditional G4/hemin DNAzyme, ensuring sensitive discrimination of MRSA (limit of detection: 9.6 pM). Assay stability and antimatrix interference capability enable clinical application, which shows compared diagnostic ability with classic methods (100% sensitivity and 100% specificity) but possesses more simplified procedures and shorter turnaround time (<6 h). This colorimetric strategy in a nonsite-specific and hypersensitive manner holds foreseeable prospects in clinical diagnostic and research applications.
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Affiliation(s)
- Xiaolin Xie
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China.,Department of Clinical Laboratory, Chongqing Ninth People's Hospital, Chongqing 400700, P.R. China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Juan Dong
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jia Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lanxin Jiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bing Liao
- Department of Clinical Laboratory, Chongqing Ninth People's Hospital, Chongqing 400700, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Qingsong Liu
- Department of Clinical Laboratory, Women and Children's Hospital in Beibei District of Chongqing, Chongqing 400700, P.R. China
| | - Fukang Luo
- Department of Clinical Laboratory, Chongqing Ninth People's Hospital, Chongqing 400700, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
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3
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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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4
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Abstract
Aptamers are single-stranded DNA or RNA molecules that can be identified through an iterative in vitro selection–amplification process. Among them, fluorogenic aptamers in response to small molecules have been of great interest in biosensing and bioimaging due to their rapid fluorescence turn-on signals with high target specificity and low background noise. In this review, we report recent advances in fluorogenic aptasensors and their applications to in vitro diagnosis and cellular imaging. These aptasensors modulated by small molecules have been implemented in different modalities that include duplex or molecular beacon-type aptasensors, aptazymes, and fluorogen-activating aptamer reporters. We highlight the working principles, target molecules, modifications, and performance characteristics of fluorogenic aptasensors, and discuss their potential roles in the field of biosensor and bioimaging with future directions and challenges.
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5
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Abstract
Catalytic DNAs (DNAzymes) with peroxidase-like activity have great potential in bioanalytical chemistry [1], owing to numerous advantages that DNA enzymes offer over conventional protein enzymes, including structural simplicity, low cost, thermal stability, and straightforward handling and preparation. Maximizing the efficiency of the peroxidase activity of such DNAzymes is a subject in need of review. In this chapter, we discuss the optimal experimental conditions for the peroxidase activity of these DNAzymes and describe general procedures for their utilization.
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6
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Köhler T, Patsis PA, Hahn D, Ruland A, Naas C, Müller M, Thiele J. DNAzymes as Catalysts for l-Tyrosine and Amyloid β Oxidation. ACS OMEGA 2020; 5:7059-7064. [PMID: 32280846 PMCID: PMC7143405 DOI: 10.1021/acsomega.9b02645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/05/2020] [Indexed: 05/03/2023]
Abstract
Single-stranded deoxyribonucleic acids have an enormous potential for catalysis by applying tailored sequences of nucleotides for individual reaction conditions and substrates. If such a sequence is guanine-rich, it may arrange into a three-dimensional structure called G-quadruplex and give rise to a catalytically active DNA molecule, a DNAzyme, upon addition of hemin. Here, we present a DNAzyme-mediated reaction, which is the oxidation of l-tyrosine toward dityrosine by hydrogen peroxide. With an optimal stoichiometry between DNA and hemin of 1:10, we report an activity of 101.2 ± 3.5 μUnits (μU) of the artificial DNAzyme Dz-00 compared to 33.0 ± 1.8 μU of free hemin. Exemplarily, DNAzymes may take part in neurodegeneration caused by amyloid beta (Aβ) aggregation due to l-tyrosine oxidation. We show that the natural, human genome-derived DNAzyme In1-sp is able to oxidize Aβ peptides with a 4.6% higher yield and a 33.3% higher velocity of the reaction compared to free hemin. As the artificial DNAzyme Dz-00 is even able to catalyze Aβ peptide oxidation with a 64.2% higher yield and 337.1% higher velocity, an in-depth screening of human genome-derived DNAzymes may identify further candidates with similarly high catalytic activity in Aβ peptide oxidation.
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Affiliation(s)
- Tony Köhler
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Panagiotis A. Patsis
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- European
Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dominik Hahn
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- Center
for Regenerative Therapies Dresden (CRTD), Fetscherstraße 105, 01307 Dresden, Germany
| | - André Ruland
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Carolin Naas
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Martin Müller
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Julian Thiele
- Leibniz-Institut
für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- E-mail:
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7
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Yum JH, Park S, Sugiyama H. G-quadruplexes as versatile scaffolds for catalysis. Org Biomol Chem 2019; 17:9547-9561. [DOI: 10.1039/c9ob01876j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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8
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Chen J, Zhang Y, Cheng M, Guo Y, Šponer J, Monchaud D, Mergny JL, Ju H, Zhou J. How Proximal Nucleobases Regulate the Catalytic Activity of G-Quadruplex/Hemin DNAzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03811] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingying Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiri Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC Dijon 21078, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, 33600 Pessac, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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9
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Peroxidyme-Amplified Radical Chain Reaction (PARCR): Visible Detection of a Catalytic Reporter. Angew Chem Int Ed Engl 2017; 56:13411-13415. [DOI: 10.1002/anie.201706163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/14/2017] [Indexed: 12/31/2022]
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10
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Goertz JP, White IM. Peroxidyme-Amplified Radical Chain Reaction (PARCR): Visible Detection of a Catalytic Reporter. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- John P. Goertz
- Department of Bioengineering; University of Maryland; College Park MD 20742 USA
| | - Ian M. White
- Department of Bioengineering; University of Maryland; College Park MD 20742 USA
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11
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Fan D, Zhu X, Dong S, Wang E. Tyramine Hydrochloride Based Label-Free System for Operating Various DNA Logic Gates and a DNA Caliper for Base Number Measurements. Chemphyschem 2017; 18:1767-1772. [DOI: 10.1002/cphc.201601291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
| | - Xiaoqing Zhu
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P.R. China
- University of Chinese Academy of Sciences; Beijing 100039 P.R. China
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12
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Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers. Sci Rep 2016; 6:33888. [PMID: 27667717 PMCID: PMC5036188 DOI: 10.1038/srep33888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/05/2016] [Indexed: 12/20/2022] Open
Abstract
A twice-as-smart ligand is a small molecule that experiences a structural switch upon interaction with its target (i.e., smart ligand) that concomitantly triggers its fluorescence (i.e., smart probe). Prototypes of twice-as-smart ligands were recently developed to track and label G-quadruplexes: these higher-order nucleic acid structures originate in the assembly of four guanine(G)-rich DNA or RNA strands, whose stability is imparted by the formation and the self-assembly of G-quartets. The first prototypes of twice-as-smart quadruplex ligands were designed to exploit the self-association of quartets, being themselves synthetic G-quartets. While their quadruplex recognition capability has been thoroughly documented, some doubts remain about the precise photophysical mechanism that underlies their peculiar spectroscopic properties. Here, we uncovered this mechanism via complete theoretical calculations. Collected information was then used to develop a novel application of twice-as-smart ligands, as efficient chemical sensors of bacterial signaling pathways via the fluorescent detection of naturally occurring extracellular quadruplexes formed by cyclic dimeric guanosine monophosphate (c-di-GMP).
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13
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Li L, Shang G, Qin W. Label-free polymerization amplified potentiometric sensing platform for radical reactions using polyion sensitive membrane electrodes as transducers. RSC Adv 2016. [DOI: 10.1039/c6ra04530h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Based on the cascade amplification abilities of radical polymerization reactions, an amplified potentiometric sensing platform for radical reactions was developed.
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Affiliation(s)
- Long Li
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research (YIC)
- Chinese Academy of Sciences (CAS)
- Shandong Provincial Key Laboratory of Coastal Environmental Processes
- YICCAS
| | - Guoliang Shang
- College of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264003
- P. R. China
| | - Wei Qin
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research (YIC)
- Chinese Academy of Sciences (CAS)
- Shandong Provincial Key Laboratory of Coastal Environmental Processes
- YICCAS
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14
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FUNABASHI H. Hemin/G-quadruplex Complex as a Signal Generator for Electrochemical Assays of Bioanalytes. ELECTROCHEMISTRY 2016. [DOI: 10.5796/electrochemistry.84.290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Hisakage FUNABASHI
- Institute for Sustainable Sciences and Development, Hiroshima University
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15
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Shumayrikh N, Huang YC, Sen D. Heme activation by DNA: isoguanine pentaplexes, but not quadruplexes, bind heme and enhance its oxidative activity. Nucleic Acids Res 2015; 43:4191-201. [PMID: 25824944 PMCID: PMC4417173 DOI: 10.1093/nar/gkv266] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 02/13/2015] [Accepted: 03/17/2015] [Indexed: 12/31/2022] Open
Abstract
Guanine-rich, single-stranded, DNAs and RNAs are able to fold to form G-quadruplexes that are held together by guanine base quartets. G-quadruplexes are known to bind ferric heme [Fe(III)-protoporphyrin IX] and to strongly activate such bound hemes toward peroxidase (1-electron oxidation) as well as oxygenase/peroxygenase (2-electron oxidation) activities. However, much remains unknown about how such activation is effected. Herein, we investigated whether G-quadruplexes were strictly required for heme activation or whether related multi-stranded DNA/RNA structures such as isoguanine (iG) quadruplexes and pentaplexes could also bind and activate heme. We found that iG-pentaplexes did indeed bind and activate heme comparably to G-quadruplexes; however, iG-quadruplexes did neither. Earlier structural and computational studies had suggested that while the geometry of backbone-unconstrained iG-quintets templated by cations such as Na(+) or NH4 (+) was planar, that of iG-quartets deviated from planarity. We hypothesize that the binding as well as activation of heme by DNA or RNA is strongly supported by the planarity of the nucleobase quartet or quintet that interacts directly with the heme.
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Affiliation(s)
- Nisreen Shumayrikh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yu Chuan Huang
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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16
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Golub E, Lu CH, Willner I. Metalloporphyrin/G-quadruplexes: From basic properties to practical applications. J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424615300025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Guanine-rich single-stranded nucleic acids self-assemble into G-quadruplex nanostructures (predominately in the presence of K +-ions). Metalloporphyrins bind to the G-quadruplex nanostructures to form supramolecular assemblies exhibiting unique catalytic, electrocatalytic and photophysical properties. This paper addresses the advances in the characterization and the implementation of the metalloporphyrin/G-quadruplexes complexes for various applications. Out of the different complexes, the most extensively studied complexes are the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme and the Zn(II) -protoporphyrin IX-functionalized G-quadruplex. Specifically, the hemin/G-quadruplex was found to act as a catalyst for driving different chemical transformations that mimic the native horseradish peroxidase enzyme, and, also, to function as an electrocatalyst for the reduction of H 2 O 2. Also, the hemin/G-quadruplex stimulates interesting photophysical and photocatalytic processes such as the electron-transfer quenching of semiconductor quantum dots or the chemiluminescence resonance energy transfer to semiconductor quantum dots. Alternatively, Zn(II) -protoporphyrin IX associated with G-quadruplexes exhibit intensified fluorescence properties. Beyond the straight forward application of the metalloporphyrin/G-quadruplexes as catalysts that stimulate different chemical transformations, the specific catalytic, electrocatalytic and photocatalytic functions of hemin/G-quadruplexes are heavily implemented to develop sophisticated colorimetric, electrochemical, and optical sensing platforms. Also, the unique fluorescence properties of Zn(II) -protoporphyrin IX-functionalized G-quadruplexes are applied to develop fluorescence sensing platforms. The article exemplifies different sensing assays for analyzing DNA, ligand-aptamer complexes and telomerase activity using the metalloporphyrins/G-quadruplexes as transducing labels. Also, the use of the hemin/G-quadruplex as a probe to follow the operations of DNA machines is discussed.
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Affiliation(s)
- Eyal Golub
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Chun-Hua Lu
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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17
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Li H, Fu HW, Zhao T, Kong DM. Simple, PCR-free telomerase activity detection using G-quadruplex–hemin DNAzyme. RSC Adv 2015. [DOI: 10.1039/c4ra14460k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A G-quadruplex DNAzyme-based telomerase activity detection method is developed by utilizing telomerase-triggered generation of short G-rich extension products.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Hai-Wei Fu
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Ting Zhao
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
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18
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Gribas AV, Korolev SP, Zatsepin TS, Gottikh MB, Sakharov IY. Structure–activity relationship study for design of highly active covalent peroxidase-mimicking DNAzyme. RSC Adv 2015. [DOI: 10.1039/c5ra03167b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We synthesized a series of conjugates of hemin and its aptamer EAD2, named covalent peroxidase-mimicking DNAzymes (PMDNAzymes), varying the length, rigidity and 5′-/3′-position of the linker between the oligonucleotide and hemin.
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Affiliation(s)
| | - Sergey P. Korolev
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
- Belozersky Institute of Physical and Chemical Biology
| | - Timofey S. Zatsepin
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
- Belozersky Institute of Physical and Chemical Biology
| | - Marina B. Gottikh
- Belozersky Institute of Physical and Chemical Biology
- Lomonosov Moscow State University
- Moscow 119991
- Russia
| | - Ivan Yu. Sakharov
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
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19
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Gribas AV, Zhao S, Sakharov IY. Improved method for chemiluminescent determination of peroxidase-mimicking DNAzyme activity. Anal Biochem 2014; 466:19-23. [DOI: 10.1016/j.ab.2014.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/08/2014] [Accepted: 07/16/2014] [Indexed: 12/20/2022]
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20
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Acetylcholinesterase-Free Colorimetric Detection of Chlorpyrifos in Fruit Juice Based on the Oxidation Reaction of H2O2 with Chlorpyrifos and ABTS2− Catalyzed by Hemin/G-Quadruplex DNAzyme. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-0042-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Yang L, Du F, Chen G, Yasmeen A, Tang Z. A novel colorimetric PCR-based biosensor for detection and quantification of hepatitis B virus. Anal Chim Acta 2014; 840:75-81. [PMID: 25086896 DOI: 10.1016/j.aca.2014.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/11/2014] [Accepted: 05/19/2014] [Indexed: 12/20/2022]
Abstract
Hepatitis B virus (HBV) can cause viral infection that attacks the liver and it is a major global health problem that put people at a high risk of death from cirrhosis of the liver and liver cancer. HBV has infected one third of the worldwide population, and 350 million people suffer from chronic HBV infection. For these reasons, development of an accurate, sensitive and expedient detection method for diagnosing, monitoring and assessing therapeutic response of HBV is very necessary and urgent for public health and disease control. Here we report a new strategy for detection of viral load quantitation of HBV based on colorimetric polymerase chain reaction (PCR) with DNAzyme-containing probe. The special DNAzyme adopting a G-quadruplex structure exhibited peroxidase-like activity in the presence of hemin to report colorimetric signal. This method has shown a broad range of linearity and high sensitivity. This study builds important foundation to achieve the specific and accurate detection level of HBV DNA with a low-cost and effective method in helping diagnosing, preventing and protecting human health form HBV generally all over the world and especially in developing countries.
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Affiliation(s)
- Li Yang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
| | - Afshan Yasmeen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China.
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22
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Aleman-Garcia MA, Orbach R, Willner I. Ion-Responsive Hemin-G-Quadruplexes for Switchable DNAzyme and Enzyme Functions. Chemistry 2014; 20:5619-24. [DOI: 10.1002/chem.201304702] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/20/2014] [Indexed: 12/28/2022]
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23
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Qi C, Zhang N, Yan J, Liu X, Bing T, Mei H, Shangguan D. Activity enhancement of G-quadruplex/hemin DNAzyme by spermine. RSC Adv 2014. [DOI: 10.1039/c3ra45429k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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24
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Wang Q, Xu N, Lei J, Ju H. Regulative peroxidase activity of DNA-linked hemin by graphene oxide for fluorescence DNA sensing. Chem Commun (Camb) 2014; 50:6714-7. [DOI: 10.1039/c4cc02273d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The inhibition effect of graphene oxide toward the peroxidase activity of DNA-linked hemin was identified for fluorescence DNA sensing.
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Affiliation(s)
- Quanbo Wang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P. R. China
| | - Nan Xu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093, P. R. China
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25
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Roembke BT, Nakayama S, Sintim HO. Nucleic acid detection using G-quadruplex amplification methodologies. Methods 2013; 64:185-98. [PMID: 24135042 PMCID: PMC7129037 DOI: 10.1016/j.ymeth.2013.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/19/2013] [Accepted: 10/02/2013] [Indexed: 12/28/2022] Open
Abstract
In the last decade, there has been an explosion in the use of G-quadruplex labels to detect various analytes, including DNA/RNA, proteins, metals and other metabolites. In this review, we focus on strategies for the detection of nucleic acids, using G-quadruplexes as detection labels or as enzyme labels that amplify detection signals. Methods to detect other analytes are briefly mentioned. We highlight various strategies, including split G-quadruplex, hemin-G-quadruplex conjugates, molecular beacon G-quadruplex or inhibited G-quadruplex probes. The tandem use of G-quadruplex labels with various DNA-modifying enzymes, such as polymerases (used for rolling circle amplification), exonucleases and endonucleases, is also discussed. Some of the detection modalities that are discussed in this review include fluorescence, colorimetric, chemiluminescence, and electrochemical methods.
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26
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Golub E, Freeman R, Willner I. Hemin/G-quadruplex-catalyzed aerobic oxidation of thiols to disulfides: application of the process for the development of sensors and aptasensors and for probing acetylcholine esterase activity. Anal Chem 2013; 85:12126-33. [PMID: 24299064 DOI: 10.1021/ac403305k] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This study describes the novel hemin/G-quadruplex DNAzyme-catalyzed aerobic oxidation of thiols to disulfides and the respective mechanism. The mechanism of the reaction involves the DNAzyme-catalyzed oxidation of thiols to disulfides and the thiol-mediated autocatalytic generation of H2O2 from oxygen. The coupling of a concomitant H2O2-mediated hemin/G-quadruplex-catalyzed oxidation of Amplex Red to the fluorescent resorufin as a transduction module provides a fluorescent signal for probing the catalyzed oxidation of the thiol to disulfides and for probing sensing processes that yield the hemin/G-quadruplex as a functional label. Accordingly, a versatile sensing method for analyzing thiols (L-cysteine, glutathione) using the H2O2-mediated DNAzyme-catalyzed oxidation of Amplex Red to the resorufin was developed. Also, the L-cysteine and Amplex Red system was implemented as an auxiliary fluorescent transduction module for probing recognition events that form the catalytic hemin/G-quadruplex structures. This is exemplified with the development of thrombin aptasensor. The thrombin/thrombin binding aptamer recognition complex binds hemin, and the resulting catalytic complex activates the auxiliary transduction module, involving the aerobic oxidation of l-cysteine and the concomitant formation of the fluorescent resorufin. Finally, the hemin/G-quadruplex DNAzyme/Amplex Red system was used to follow the activity of acetylcholine esterase, AChE, and to probe its inhibition. The AChE-catalyzed hydrolysis of acetylthiocholine to the thiol-functionalized thiocholine enabled the probing of the enzymatic activity of AChE through the hemin/G-quadruplex-catalyzed aerobic oxidation of thiocholine to the respective disulfide and the concomitant generation of the fluorescent resorufin product.
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Affiliation(s)
- Eyal Golub
- The Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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27
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Kong DM. Factors influencing the performance of G-quadruplex DNAzyme-based sensors. Methods 2013; 64:199-204. [DOI: 10.1016/j.ymeth.2013.07.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 07/08/2013] [Indexed: 02/03/2023] Open
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28
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Cai Y, Li N, Kong DM, Shen HX. Fluorogenic substrate screening for G-quadruplex DNAzyme-based sensors. Biosens Bioelectron 2013; 49:312-7. [DOI: 10.1016/j.bios.2013.05.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
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29
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Bo H, Wang C, Gao Q, Qi H, Zhang C. Selective, colorimetric assay of glucose in urine using G-quadruplex-based DNAzymes and 10-acetyl-3,7-dihydroxy phenoxazine. Talanta 2013; 108:131-5. [DOI: 10.1016/j.talanta.2013.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 03/01/2013] [Accepted: 03/01/2013] [Indexed: 01/29/2023]
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30
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Du F, Streckenbach F, Chen H, Huang X, Tang Z, Marx A. RNA pathogen detection with one-step reverse transcription PCR and strand-displacement based signal amplification. Analyst 2013; 138:1544-8. [PMID: 23348105 DOI: 10.1039/c2an36688f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A novel detection method for RNA pathogens based on one-step reverse transcription PCR is introduced here. This method utilized the reverse transcriptase activity and the 5'-nuclease activity of TaqM1 DNA polymerase to transform target RNA into cDNA. The following PCR process released a fragment from the 5' end as a specific probe. Afterwards this fragment triggered a strand-displacement based signal amplification to release large amounts of G-quadruplex DNAzymes. All the probes applied in our method were unmodified DNA oligonucleotides. The detection results could be reported without sophisticated instruments either in the colorimetric way through oxidizing ABTS or in the fluorometric way by using tyramine as substrate. This approach could successfully detect HIV-1 in a blood sample and it has a linear concentration range of 6 fM to 60 pM.
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Affiliation(s)
- Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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31
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Zhou L, Du F, Zhao Y, Yameen A, Chen H, Tang Z. DNAzyme based gap-LCR detection of single-nucleotide polymorphism. Biosens Bioelectron 2013; 45:141-7. [PMID: 23455054 DOI: 10.1016/j.bios.2013.01.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/24/2013] [Accepted: 01/30/2013] [Indexed: 11/18/2022]
Abstract
Fast and accurate detection of single-nucleotide polymorphism (SNP) is thought more and more important for understanding of human physiology and elucidating the molecular based diseases. A great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. However most of those methods developed to date incorporate complicated probe labeling and depend on advanced equipment. The DNAzyme based Gap-LCR detection method averts any chemical modification on probes and circumvents those problems by incorporating a short functional DNA sequence into one of LCR primers. Two kinds of exonuclease are utilized in our strategy to digest all the unreacted probes and release the DNAzymes embedded in the LCR product. The DNAzyme applied in our method is a versatile tool to report the result of SNP detection in colorimetric or fluorometric ways for different detection purposes.
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Affiliation(s)
- Li Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
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32
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Zhou Z, Zhu J, Zhang L, Du Y, Dong S, Wang E. G-quadruplex-Based Fluorescent Assay of S1 Nuclease Activity and K+. Anal Chem 2013; 85:2431-5. [DOI: 10.1021/ac303440d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Jinbo Zhu
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Libing Zhang
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Yan Du
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Shaojun Dong
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Erkang Wang
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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33
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Wang X, Ding Z, Ren Q, Qin W. Polymeric Membrane Neutral Phenol-Sensitive Electrodes for Potentiometric G-Quadruplex/Hemin DNAzyme-Based Biosensing. Anal Chem 2013; 85:1945-50. [DOI: 10.1021/ac3035629] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Xuewei Wang
- Key Laboratory of Coastal Zone
Environmental Processes, Yantai Institute of Coastal Zone Research
(YIC), Chinese Academy of Sciences (CAS);
Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes,
YICCAS, Yantai 264003, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhaofeng Ding
- College of Chemistry and Chemical
Engineering, Yantai University, Yantai
264003, P. R. China
| | - Qingwei Ren
- College of Chemistry and Chemical
Engineering, Yantai University, Yantai
264003, P. R. China
| | - Wei Qin
- Key Laboratory of Coastal Zone
Environmental Processes, Yantai Institute of Coastal Zone Research
(YIC), Chinese Academy of Sciences (CAS);
Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes,
YICCAS, Yantai 264003, P. R. China
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34
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Nakayama S, Sintim HO. Investigating the interactions between cations, peroxidation substrates and G-quadruplex topology in DNAzyme peroxidation reactions using statistical testing. Anal Chim Acta 2012; 747:1-6. [PMID: 22986129 DOI: 10.1016/j.aca.2012.08.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/28/2012] [Accepted: 08/08/2012] [Indexed: 12/11/2022]
Abstract
Cations affect the topology and enzymatic proficiency of most macromolecular catalysts but the role of cations in DNAzyme peroxidation reactions remains unresolved. Herein, we use statistical methods (ANOVA, t-test and Wilcoxon Mann-Whitney non-parametric test) to demonstrate that there are strong associations between cations, DNAzyme topology, peroxidation substrate and peroxidation rates of G-quadruplex peroxidises. Ammonium cation was found to be superior to all tested cations, including potassium. A t-test indicated that NH(4)(+) was better than K(+) with a p-value=0.05. Interestingly, the nature of the peroxidation substrate employed affected the dependence of peroxidation rate on the cation present and of the three substrates tested, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS), tyramine and 3,3',5,5'-tetramethylbenzidine (TMB), ABTS was the most sensitive to the nature of cation present.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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35
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Dong J, Cui X, Deng Y, Tang Z. Amplified detection of nucleic acid by G-quadruplex based hybridization chain reaction. Biosens Bioelectron 2012; 38:258-63. [PMID: 22739472 DOI: 10.1016/j.bios.2012.05.042] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/29/2012] [Accepted: 05/30/2012] [Indexed: 01/29/2023]
Abstract
A protein-free, isothermal, self-amplified nucleic acid sensing system which was a G-quadruplex integrated hybridization chain reaction (GQ-HCR) system was developed. The G-quadruplex was closed two-thirds in the loop and one-third in the stem of one of the GQ-HCR hairpin probes. In the absence of the target molecule, the GQ-HCR probes stayed as inactive meta-stable hairpin structures and the G-quadruplex was inert. Reversely, the GQ-HCR probes could be cross-opened to start a hybridization chain reaction and the closed G-quadruplex could be released to be free when the GQ-HCR probes came across the target molecule. The GQ-HCR nucleic acid sensing system could detect as low as 7.5 nM ssDNA or RNA by the colorimetric method and 4 nM ssDNA by the fluorometric method. Less than 10 copies of dsDNA template could also be detected when PCR was combined with the GQ-HCR system (PCR+GQ-HCR). Because of these advantages, the GQ-HCR system was also studied for application in visual chip detection to obtain a satisfactory repeatable and specific result.
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Affiliation(s)
- Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Sichuan, Chengdu 610041, PR China
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36
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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37
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Golub E, Freeman R, Willner I. A hemin/G-quadruplex acts as an NADH oxidase and NADH peroxidase mimicking DNAzyme. Angew Chem Int Ed Engl 2012; 50:11710-4. [PMID: 22229160 DOI: 10.1002/anie.201103853] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Eyal Golub
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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38
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Zhou Z, Du Y, Zhang L, Dong S. A label-free, G-quadruplex DNAzyme-based fluorescent probe for signal-amplified DNA detection and turn-on assay of endonuclease. Biosens Bioelectron 2012; 34:100-5. [PMID: 22366377 DOI: 10.1016/j.bios.2012.01.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 11/30/2011] [Accepted: 01/19/2012] [Indexed: 11/28/2022]
Abstract
A novel G-quadruplex DNAzyme molecular beacon (G-DNAzymeMB) strategy is developed for assays of target DNA and restriction endonuclease. The detection system consists of G-DNAzymeMB strand and a blocker DNA by using the fluorescence of 2',7'-dichlorodihydrofluorescein diacetate (H(2)DCFDA) catalyzed by G-DNAzymeMB as a signal reporter. G-DNAzymeMB exhibits peroxidase activity in its free hairpin structure, and forms a catalytically inactive hybrid when hybridized with blocker DNA. Upon displacement of blocker DNA by target DNA or cleavage by restriction endonuclease, G-DNAzymeMB is released and two lateral portions of G-DNAzymeMB form a G-quadruplex structure, resulting in the recovery of catalytic activity which acts as a cofactor to catalyze H(2)O(2)-mediated oxidation of H(2)DCFDA. For DNA detection system, exonuclease III (Exo III)-catalyzed amplification strategy is introduced to improve the sensitivity and target DNA could be detected as low as 0.1 pM. With respect to restriction endonuclease detection system, 0.1 U/mL EcoRI endonuclease could be detected and this method could be easily transported to other restriction endonuclease analysis by simply changing the recognition sequence. These results demonstrate that the proposed G-DNAzymeMB strategy could be used as a label-free, simple, sensitive and cost-effective approach in analysis of target DNA and restriction endonuclease.
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Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, People's Republic of China
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39
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Nakayama S, Roelofs K, Lee VT, Sintim HO. A C-di-GMP-proflavine-hemin supramolecular complex has peroxidase activity--implication for a simple colorimetric detection. MOLECULAR BIOSYSTEMS 2012; 8:726-9. [PMID: 22252690 DOI: 10.1039/c2mb05430b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Herein, we demonstrate that the bacterial signaling molecule, c-di-GMP, can enhance the peroxidation of hemin when proflavine is present. The c-di-GMP-proflavine-hemin nucleotidezyme can oxidize the colorless compound 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS, to the colored radical cation ABTS˙(+) and hence provides simple colorimetric detection of c-di-GMP at low micromolar concentrations.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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40
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Yang X, Fang C, Mei H, Chang T, Cao Z, Shangguan D. Characterization of G-quadruplex/hemin peroxidase: substrate specificity and inactivation kinetics. Chemistry 2011; 17:14475-84. [PMID: 22106035 DOI: 10.1002/chem.201101941] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Indexed: 02/05/2023]
Abstract
Recently, G-quadruplex/hemin (G4/hemin) complexes have been found to exhibit peroxidase activity, and this feature has been extensively exploited for colorimetric detection of various targets. To further understand and characterize this important DNAzyme, its substrate specificity, inactivation mechanism, and kinetics have been examined by comparison with horseradish peroxidase (HRP). G4/hemin DNAzyme exhibits broader substrate specificity and much higher inactivation rate than HRP because of the exposure of the catalytic hemin center. The inactivation of G4/hemin DNAzyme is mainly attributed to the degradation of hemin by H(2)O(2) rather than the destruction of G4. Both the inactivation rate and catalytic oxidation rate of G4/hemin DNAzyme depend on the concentration of H(2)O(2), which suggests that active intermediates formed by G4/hemin and H(2)O(2) are the branch point of catalysis and inactivation. Reducing substrates greatly inhibit the inactivation of G4/hemin DNAzyme by rapidly reacting with the active intermediates. A possible catalytic and inactivation process of G4/hemin has been proposed. These results imply a potential cause for the hemin-mediated cellular injury and provide insightful information for the future application of G4/hemin DNAzyme.
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Affiliation(s)
- Xiaojuan Yang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, PR China
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41
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Golub E, Freeman R, Willner I. A Hemin/G-Quadruplex Acts as an NADH Oxidase and NADH Peroxidase Mimicking DNAzyme. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103853] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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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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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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Golub E, Freeman R, Niazov A, Willner I. Hemin/G-quadruplexes as DNAzymes for the fluorescent detection of DNA, aptamer-thrombin complexes, and probing the activity of glucose oxidase. Analyst 2011; 136:4397-401. [PMID: 21881641 DOI: 10.1039/c1an15596b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hemin/G-quadruplex catalyzes the H(2)O(2)-mediated oxidation of Amplex Red to the fluorescent product resorufin. This process is implemented to develop hairpin nucleic acid structures for the detection of DNA, to probe the catalytic activity of glucose oxidase, to use the thrombin-aptamer complex as a catalytic readout structure, and to quantitatively analyze telomere chain composition.
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Affiliation(s)
- Eyal Golub
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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Zhang Y, Li B, Jin Y. Label-free fluorescent detection of thrombin using G-quadruplex-based DNAzyme as sensing platform. Analyst 2011; 136:3268-73. [PMID: 21725571 DOI: 10.1039/c1an00002k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a label-free and sensitive fluorescent method for detection of thrombin using a G-quadruplex-based DNAzyme as the sensing platform. The thrombin-binding aptamer (TBA) is able to bind hemin to form the G-quadruplex-based DNAzyme, and thrombin can significantly enhance the activity of the G-quadruplex-based DNAzyme. The G-quadruplex-based DNAzyme is found to effectively catalyze the H(2)O(2)-mediated oxidation of thiamine, giving rise to fluorescence emission. This allows us to utilize the H(2)O(2)-thiamine fluorescent system for the quantitative analysis of thrombin. The assay shows a linear toward thrombin concentration in the range of 0.01-0.12 nM. The present limit of detection for thrombin is 1 pM, and the sensitivity for analyzing thrombin is improved by about 10,000-fold as compared with the reported colorimetric counterpart. The work also demonstrates that thiamine is an excellent substrate for the fluorescence assay using the G-quadruplex-based DNAzyme as the sensing platform.
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Affiliation(s)
- Yuanfu Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi'an, 710062, PR China
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G-quadruplex DNAzyme-based microcystin-LR (toxin) determination by a novel immunosensor. Biosens Bioelectron 2011; 26:4393-8. [DOI: 10.1016/j.bios.2011.04.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/25/2011] [Accepted: 04/25/2011] [Indexed: 01/13/2023]
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Nakayama S, Wang J, Sintim HO. DNA-based peroxidation catalyst--what is the exact role of topology on catalysis and is there a special binding site for catalysis? Chemistry 2011; 17:5691-8. [PMID: 21469226 DOI: 10.1002/chem.201002349] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 01/19/2011] [Indexed: 12/11/2022]
Abstract
In the last decade, there has been growing interests in studies aimed at delineating the strategies used by various nucleic acid enzymes to facilitate catalysis. Insights gained from such studies would enable the design of better DNA/RNA catalysts for various applications such as biosensing. DNA and RNA catalysts have been shown to be able to catalyze myriads of reactions, including peroxidation reactions, which are catalyzed by G-quadruplexes. In this report, we provide data that clarifies how G-quadruplex peroxidases achieve catalysis. Firstly, we show that by covalently linking a hemin cofactor to DNAzymes, anti-parallel G-quadruplexes, which have been previously shown to be catalytically inefficient, can be "resurrected" to become good peroxidation catalysts. We also reveal that the relative rates of peroxidation by DNAzyme peroxidases depend on the nature of the organic reductant, arguing for a special binding site in the peroxidase-mimicking DNAzymes for catalysis.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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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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Qiu B, Zheng ZZ, Lu YJ, Lin ZY, Wong KY, Chen GN. G-quadruplex DNAzyme as the turn on switch for fluorimetric detection of genetically modified organisms. Chem Commun (Camb) 2011; 47:1437-9. [DOI: 10.1039/c0cc02933e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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