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Brückner S, Müller F, Schadowski L, Kalle T, Weber S, Marino EC, Kutscher B, Möller AM, Adler S, Begerow D, Steinchen W, Bange G, Narberhaus F. (p)ppGpp and moonlighting RNases influence the first step of lipopolysaccharide biosynthesis in Escherichia coli. MICROLIFE 2023; 4:uqad031. [PMID: 37426605 PMCID: PMC10326835 DOI: 10.1093/femsml/uqad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/12/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023]
Abstract
The outer membrane (OM) protects Gram-negative bacteria from harsh environmental conditions and provides intrinsic resistance to many antimicrobial compounds. The asymmetric OM is characterized by phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. Previous reports suggested an involvement of the signaling nucleotide ppGpp in cell envelope homeostasis in Escherichia coli. Here, we investigated the effect of ppGpp on OM biosynthesis. We found that ppGpp inhibits the activity of LpxA, the first enzyme of LPS biosynthesis, in a fluorometric in vitro assay. Moreover, overproduction of LpxA resulted in elongated cells and shedding of outer membrane vesicles (OMVs) with altered LPS content. These effects were markedly stronger in a ppGpp-deficient background. We further show that RnhB, an RNase H isoenzyme, binds ppGpp, interacts with LpxA, and modulates its activity. Overall, our study uncovered new regulatory players in the early steps of LPS biosynthesis, an essential process with many implications in the physiology and susceptibility to antibiotics of Gram-negative commensals and pathogens.
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Affiliation(s)
- Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Fabian Müller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Laura Schadowski
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Tyll Kalle
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Sophia Weber
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Sabine Adler
- Evolution of Plants and Fungi, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
| | - Dominik Begerow
- Evolution of Plants and Fungi, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, Germany
- Organismische Botanik und Mykologie, Institut für Planzenwissenschaften und Mikrobiologie, Fachbereich Biologie, Universität Hamburg,Ohnhorststrasse 18, Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Strasse 14, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Strasse 14, Marburg, Germany
| | - Franz Narberhaus
- Corresponding author. Faculty of Biology and Biotechnology, Microbial Biology, Ruhr University Bochum, Universitätsstrasse 150, NDEF 06/784, 44780 Bochum, Germany. Tel: +492343223100; Fax: +492343214620; E-mail:
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2
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Wang X, Chen Y, Ma L, Han Z, Liu Y, Qiao J. An amplification-free CRISPR/Cas12a-based fluorescence assay for ultrasensitive detection of nuclease activity. Talanta 2023; 257:124329. [PMID: 36801553 DOI: 10.1016/j.talanta.2023.124329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/10/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Nuclease, such as RNase H and DNase I, plays key roles in plenty of cellular processes and could be potential therapeutic target for drug development. It is necessary to establish rapid and simple-to-use methods to detect nuclease activity. Herein, we develop a Cas12a-based fluorescence assay without any nucleic acid amplification steps for ultrasensitive detection of RNase H or DNase I activity. By our design, the pre-assembled crRNA/ssDNA duplex triggered the cleavage of fluorescent probes in the presence of Cas12a enzymes. However, the crRNA/ssDNA duplex was selectively digested with the addition of RNase H or DNase I, which leaded to fluorescence intensity changes. Under optimized conditions, the method exhibited good analytical performance, achieving a limit of detection (LOD) as low as 0.0082 U/mL for RNase H and 0.13 U/mL for DNase I, respectively. The method was feasible for analysis of RNase H in human serum and cell lysates, as well as for screening of enzyme inhibitors. Moreover, it can be adopted to image RNase H activity in living cells. Together, this study provides a facile platform for nuclease detection and could be expanded for other biomedical research and clinical diagnostics.
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Affiliation(s)
- Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Yichuan Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | | | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China; BravoVax Co., Ltd., Wuhan, Hubei, China.
| | - Jie Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China; School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China.
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3
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Shi Y, Chen C, Zhang Y, Dong Y, Wang S. Electrogenerated chemiluminescence resonance energy transfer between luminol and MnO 2 nanosheets decorated with Cu 2O nanoparticles for sensitive detection of RNase H. Analyst 2023; 148:1300-1308. [PMID: 36847286 DOI: 10.1039/d3an00002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In the present work, a novel approach was developed for the preparation of Cu2O nanoparticle decorated MnO2 nanosheets (Cu2O@MnO2). Uniformly dispersed Cu2O nanocrystals were produced on the surface of MnO2 nanosheets by in situ reduction under refluxing conditions. The unique structure of the used MnO2 nanosheet support played a vital role in the preparation of such Cu2O@MnO2 nanocomposites. The electrogenerated chemiluminescence (ECL) resonance energy transfer can occur between the luminol/H2O2 system and Cu2O@MnO2 nanocomposites, resulting in a decrease of the ECL intensity, which can be used to fabricate an ECL sensor. Cu2O@MnO2 nanocomposite modified heterologous DNA/RNA duplexes were modified on the GCE to construct an ECL-RET system, leading to the decrease of ECL intensity. As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA/RNA strands to release Cu2O@MnO2 nanocomposites and recover the ECL signal. As a result, an "off-on" mode ECL sensor for sensitive RNase H assay was fabricated. Under the optimal conditions, the detection limit of RNase H is 0.0005 U mL-1, which is superior to other approaches. The proposed method provides a universal platform for monitoring RNase H, and exhibits great potential in bioanalysis.
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Affiliation(s)
- Yahao Shi
- School of Chemistry and Chemical Engineering, Institute of Engineering, Anhui University of Technology, Maanshan, Anhui 243002, China.
| | - Chunting Chen
- School of Chemistry and Chemical Engineering, Institute of Engineering, Anhui University of Technology, Maanshan, Anhui 243002, China.
| | - Yahui Zhang
- School of Chemistry and Chemical Engineering, Institute of Engineering, Anhui University of Technology, Maanshan, Anhui 243002, China.
| | - Yongping Dong
- School of Chemistry and Chemical Engineering, Institute of Engineering, Anhui University of Technology, Maanshan, Anhui 243002, China.
| | - Shangbing Wang
- School of Chemistry and Chemical Engineering, Institute of Engineering, Anhui University of Technology, Maanshan, Anhui 243002, China.
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4
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Dong J, Willner I. Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis. ACS NANO 2023; 17:687-696. [PMID: 36576858 PMCID: PMC9836355 DOI: 10.1021/acsnano.2c10108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.
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Xie Z, Chen S, Zhang W, Zhao S, Zhao Z, Wang X, Huang Y, Yi G. A novel fluorescence amplification strategy combining cascade primer exchange reaction with CRISPR/Cas12a system for ultrasensitive detection of RNase H activity. Biosens Bioelectron 2022; 206:114135. [DOI: 10.1016/j.bios.2022.114135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 12/16/2022]
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6
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Kim H, Lee S, Lee J, Park HG. CRISPR/Cas12a collateral cleavage activity for an ultrasensitive assay of RNase H. Chem Commun (Camb) 2022; 58:2654-2657. [PMID: 34981101 DOI: 10.1039/d1cc06026k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We herein describe an ultrasensitive RNase H assay by utilizing CRISPR/Cas12a collateral cleavage activity. Based on this unique design principle, the RNase H activity was successfully determined down to 0.00024 U mL-1, which is quite superior to those of alternative approaches.
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jinhwan Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
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7
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Recent Advancements in Polythiophene-Based Materials and their Biomedical, Geno Sensor and DNA Detection. Int J Mol Sci 2021; 22:ijms22136850. [PMID: 34202199 PMCID: PMC8268102 DOI: 10.3390/ijms22136850] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/20/2021] [Accepted: 06/20/2021] [Indexed: 11/17/2022] Open
Abstract
In this review, the unique properties of intrinsically conducting polymer (ICP) in biomedical engineering fields are summarized. Polythiophene and its valuable derivatives are known as potent materials that can broadly be applied in biosensors, DNA, and gene delivery applications. Moreover, this material plays a basic role in curing and promoting anti-HIV drugs. Some of the thiophene’s derivatives were chosen for different experiments and investigations to study their behavior and effects while binding with different materials and establishing new compounds. Many methods were considered for electrode coating and the conversion of thiophene to different monomers to improve their functions and to use them for a new generation of novel medical usages. It is believed that polythiophenes and their derivatives can be used in the future as a substitute for many old-fashioned ways of creating chemical biosensors polymeric materials and also drugs with lower side effects yet having a more effective response. It can be noted that syncing biochemistry with biomedical engineering will lead to a new generation of science, especially one that involves high-efficiency polymers. Therefore, since polythiophene can be customized with many derivatives, some of the novel combinations are covered in this review.
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8
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Zhao H, Liu Y, Cui J, Yang C, Gao N, Jing J, Zhang X. Enzyme-triggered DNA nanomimosa: A ratiometric nanoprobe for RNase H activity sensing in living cells. Talanta 2021; 233:122547. [PMID: 34215050 DOI: 10.1016/j.talanta.2021.122547] [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: 02/06/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/24/2022]
Abstract
Since ribonuclease H (RNase H) exhibits its importance in a variety of cellular processes. It is necessary to establish strategy for RNase H detection. In this work, we are enlightened by mimosa, a natural plant which can fold in response to stimuli, to construct a DNA tetrahedron-based nanoprobe, termed DNA nanomimosa, to sensing RNase H activity based on fluorescent resonance energy transfer (FRET). The DNA nanomimosa was self-assembled from four DNA chains and one RNA chain. One of the four DNA chains contains a FRET-paired fluorophores-labeled hairpin DNA structures which is unfolded by the RNA chain through hybridization. Without RNase H, the RNA chain separate the two FRET-paired fluorophores in hairpin DNA structure, giving a feeble FRET signal. However, the presence of RNase H can selectively digest the RNA strand in RNA/unfolded-hairpin DNA section, resulting in the hairpin DNA configuration changed from "unfolded" state to "folded" state and further turn on the FRET signal. The DNA nanomimosa can be applied to achieve the determination of RNase H activity by recording the emission intensity of donor and acceptor fluorophores. This strategy shows a low detection limit by 0.017 U/mL, good specificity, and distinct advantages like the self-delivery ability, good biocompatibility, and the capacity to minimize the effects of fluctuations. This design provides a potential application in ribonuclease research and could be expanded for other biomedical research and clinical diagnostics.
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Affiliation(s)
- Hengzhi Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Yazhou Liu
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Jie Cui
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Chunlei Yang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Na Gao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Jing Jing
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xiaoling Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China.
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9
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Cleavable hairpin beacon-enhanced fluorescence detection of nucleic acid isothermal amplification and smartphone-based readout. Sci Rep 2020; 10:18819. [PMID: 33139727 PMCID: PMC7608614 DOI: 10.1038/s41598-020-75795-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/20/2020] [Indexed: 01/11/2023] Open
Abstract
Fluorescence detection of nucleic acid isothermal amplification utilizing energy-transfer-tagged oligonucleotide probes provides a highly sensitive and specific method for pathogen detection. However, currently available probes suffer from relatively weak fluorescence signals and are not suitable for simple, affordable smartphone-based detection at the point of care. Here, we present a cleavable hairpin beacon (CHB)-enhanced fluorescence detection for isothermal amplification assay. The CHB probe is a single fluorophore-tagged hairpin oligonucleotide with five continuous ribonucleotides which can be cleaved by the ribonuclease to specifically initiate DNA amplification and generate strong fluorescence signals. By coupling with loop-mediated isothermal amplification (LAMP), the CHB probe could detect Borrelia burgdorferi (B. burgdorferi) recA gene with a sensitivity of 100 copies within 25 min and generated stronger specific fluorescence signals which were easily read and analysed by our programmed smartphone. Also, this CHB-enhanced LAMP (CHB-LAMP) assay was successfully demonstrated to detect B. burgdorferi DNA extracted from tick species, showing comparable results to real-time PCR assay. In addition, our CHB probe was compatible with other isothermal amplifications, such as isothermal multiple-self-matching-initiated amplification (IMSA). Therefore, CHB-enhanced fluorescence detection is anticipated to facilitate the development of simple, sensitive smartphone-based point-of-care pathogen diagnostics in resource-limited settings.
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10
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Wang Y, Hu N, Liu C, Nie C, He M, Zhang J, Yu Q, Zhao C, Chen T, Chu X. An RNase H-powered DNA walking machine for sensitive detection of RNase H and the screening of related inhibitors. NANOSCALE 2020; 12:1673-1679. [PMID: 31894217 DOI: 10.1039/c9nr07550j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ribonuclease H (RNase H), an intracellular ribonuclease, plays a crucial role in cellular processes and especially relates to many disease processes. Here, we report a novel signal amplification strategy based on an RNase H-powered DNA walking machine for specific and sensitive RNase H activity detection. The DNA walking machine is composed of a small quantity of DNA walker strands and abundant FAM-labeled DNA-RNA chimeric strands on a single gold nanoparticle (AuNP). RNase H can specifically degrade the RNA fragment in a DNA-RNA hybrid duplex and trigger the autonomous movement of a DNA walker strand on the AuNP surface. During this process, each step of the walking can release the FAM-labeled RNA from the surface of the AuNP, realizing the signal amplification for RNase H sensing. This method has been successfully utilized for RNase H activity detection in a complex system and applied for screening of related inhibitors. Therefore, our RNase H-powered DNA walking machine gives a novel platform for RNase H activity detection and RNase H-associated drug discovery.
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Affiliation(s)
- Yafang Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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11
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Hu N, Wang Y, Liu C, He M, Nie C, Zhang J, Yu Q, Zhao C, Chen T, Chu X. An enzyme-initiated DNAzyme motor for RNase H activity imaging in living cell. Chem Commun (Camb) 2020; 56:639-642. [DOI: 10.1039/c9cc08692g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A signal amplification strategy based on an enzyme-initiated DNAzyme motor for sensitive imaging of RNase H activity in living cell.
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12
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Zhou Y, Zhang J, Jiang Q, Lu J. An allosteric switch-based hairpin for label-free chemiluminescence detection of ribonuclease H activity and inhibitors. Analyst 2019; 144:1420-1425. [PMID: 30607414 DOI: 10.1039/c8an02006j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To assay enzyme activities and screen its inhibitors, we demonstrated a novel label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure was a DNA-RNA chimeric strand, which contained a streptavidin aptamer sequence and a blocked RNA sequence. RNase H could specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer which could be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal was generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer. This novel assay method exhibited a good linear relationship in the range of 0.1-10 U mL-1 under the optimized conditions. Our results suggested that the developed system was a promising platform for monitoring the RNase H activity and showed great potential in biomedical studies and drug screening.
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Affiliation(s)
- Ying Zhou
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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Jung Y, Lee CY, Park KS, Park HG. Target-Activated DNA Polymerase Activity for Sensitive RNase H Activity Assay. Biotechnol J 2019; 14:e1800645. [PMID: 30791223 DOI: 10.1002/biot.201800645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/11/2018] [Indexed: 01/07/2023]
Abstract
Herein, the ribonuclease H (RNase H) activity assay based on the target-activated DNA polymerase activity is described. In this method, a detection probe composed of two functional sequences, a binding site for DNA polymerase and a catalytic substrate for RNase H, serves as a key component. The detection probe, at its initial state, suppresses the DNA polymerase activity, but it becomes destabilized by RNase H, which specifically hydrolyzes RNA in RNA/DNA hybrid duplexes. As a result, DNA polymerase recovers its activity and initiates multiple primer extension reactions in a separate TaqMan probe-based signal transduction module, leading to a significantly enhanced fluorescence "turn-on" signal. This assay can detect RNase H activity as low as 0.016 U mL-1 under optimized conditions. Furthermore, its potential use for evaluating RNase H inhibitors, which have been considered potential therapeutic agents against acquired immune deficiency syndrome (AIDS), is successfully explored. In summary, this approach is quite promising for the sensitive and accurate determination of enzyme activity and inhibitor screening.
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Affiliation(s)
- Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Chang Y Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ki S Park
- Department of Biological Engineering, College of Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hyun G Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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Tong C, Zhou T, Zhao C, Yuan L, Xu Y, Liu B, Fan J, Li D, Zhu A. Fluorometric determination of RNase H via a DNAzyme conjugated to reduced graphene oxide, and its application to screening for inhibitors and activators. Mikrochim Acta 2019; 186:335. [DOI: 10.1007/s00604-019-3425-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
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15
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Agarwal S, Franco E. Enzyme-Driven Assembly and Disassembly of Hybrid DNA-RNA Nanotubes. J Am Chem Soc 2019; 141:7831-7841. [PMID: 31042366 DOI: 10.1021/jacs.9b01550] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Living cells have the ability to control the dynamics of responsive assemblies such as the cytoskeleton by temporally activating and deactivating inert precursors. While DNA nanotechnology has demonstrated many synthetic supramolecular assemblies that rival biological ones in size and complexity, dynamic control of their formation is still challenging. Taking inspiration from nature, we developed a DNA-RNA nanotube system whose assembly and disassembly can be temporally controlled at physiological temperature using transcriptional programs. Nanotubes assemble when inert DNA monomers are directly and selectively activated by RNA molecules that become embedded in the structure, producing hybrid DNA-RNA assemblies. The reactions and molecular programs controlling nanotube formation are fueled by enzymes that produce or degrade RNA. We show that the speed of assembly and disassembly of the nanotubes can be controlled by tuning various reaction parameters in the transcriptional programs. We anticipate that these hybrid structures are a starting point to build integrated biological circuits and functional scaffolds inside natural and artificial cells, where RNA produced by gene networks could fuel the assembly of nucleic acid components on demand.
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Affiliation(s)
- Siddharth Agarwal
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
| | - Elisa Franco
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
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Wu K, Ma C, Deng Z, Fang N, Tang Z, Zhu X, Wang K. Label-free and nicking enzyme-assisted fluorescence signal amplification for RNase H determination based on a G-quadruplexe/thioflavin T complex. Talanta 2018; 182:142-147. [PMID: 29501133 DOI: 10.1016/j.talanta.2018.01.075] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/13/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022]
Abstract
In this paper, we describe a novel, label-free and nicking enzyme-assisted fluorescence signal amplification strategy that demonstrates to be cost efficient, sensitive, and unique for assaying the RNase H activity and inhibition based on G-quadruplex formation using a thioflavin T (ThT) dye. This novel assay method is able to detect RNase H with a detection limit of 0.03 U /mL and further exhibits a good linearity R2 = 0.9923 at a concentration range of 0.03-1 U/mL under optimized conditions. Moreover, the inhibition effect of gentamycin on the RNase H activity is also studied. This strategy provides a potential tool for the biochemical enzyme analysis and inhibitor screening.
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Affiliation(s)
- Kefeng Wu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Zhiyi Deng
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Zhenwei Tang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xingxing Zhu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China
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17
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Lee CY, Kang KS, Park KS, Park HG. Determination of RNase H activity via real-time monitoring of target-triggered rolling circle amplification. Mikrochim Acta 2017; 185:53. [DOI: 10.1007/s00604-017-2610-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
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18
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Lee CY, Jang H, Park KS, Park HG. A label-free and enzyme-free signal amplification strategy for a sensitive RNase H activity assay. NANOSCALE 2017; 9:16149-16153. [PMID: 28980684 DOI: 10.1039/c7nr04060a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We herein describe a label-free and enzyme-free signal amplification strategy for the sensitive determination of ribonuclease H (RNase H) activity, which relies on the target-triggered catalytic hairpin assembly (CHA) in conjunction with a G-quadruplex specific fluorescent binder, N-methyl mesoporphyrin IX (NMM). In the absence of RNase H, the RNA/DNA duplex serving as a substrate for RNase H cannot initiate the execution of CHA that produces G-quadruplexes; so NMM shows a low fluorescence signal. In contrast, the presence of RNase H that degrades RNA in the RNA/DNA duplex releases DNA designed to function as the catalyst for CHA. This consequently promotes the efficient CHA and generates a large number of G-quadruplexes with a significantly enhanced fluorescence signal from NMM. Based on this label-free and enzyme-free signal amplification strategy, we successfully determined the RNase H activity with a detection limit of 0.037 U mL-1 and screened potential RNase H inhibitors. Our results suggest that the developed system is a promising platform for a cost-effective, sensitive enzyme activity assay and inhibitor screening.
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Affiliation(s)
- Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-338, Republic of Korea.
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19
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An end-point method based on graphene oxide for RNase H analysis and inhibitors screening. Biosens Bioelectron 2016; 90:103-109. [PMID: 27886596 DOI: 10.1016/j.bios.2016.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/03/2016] [Accepted: 11/12/2016] [Indexed: 12/12/2022]
Abstract
As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10-3 units/ mL under optimal conditions. We demonstrate the utility of the assay by screening antibiotics, resulting in the identification of gentamycin, streptomycin and kanamycin as inhibitors with IC50 of 60±5µM, 70±8µM and 300±20µM, respectively. Furthermore, the assay was reliably used to detect RNase H in complicated biosamples and found that RNase H activity in tumor cells was inhibited by gentamycin and streptomycin sulfate in a concentration-dependent manner. The average level of RNase H in serums of HBV infection group was similar to that of control group. In summary, the assay provides an alternative tool for biochemical analysis for this enzyme and indicates the feasibility of high throughput screening inhibitors of RNase H in vitro and in vivo.
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20
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Petzold C, Marceau AH, Miller KH, Marqusee S, Keck JL. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity. J Biol Chem 2015; 290:14626-36. [PMID: 25903123 PMCID: PMC4505529 DOI: 10.1074/jbc.m115.655134] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/16/2015] [Indexed: 12/21/2022] Open
Abstract
Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome.
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Affiliation(s)
- Christine Petzold
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
| | - Aimee H Marceau
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
| | - Katherine H Miller
- California Institute for Quantitative Biosciences, QB3 and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, QB3 and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - James L Keck
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
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21
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A hybrid chimeric system for versatile and ultra-sensitive RNase detection. Sci Rep 2015; 5:9558. [PMID: 25828752 PMCID: PMC4381352 DOI: 10.1038/srep09558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/11/2015] [Indexed: 12/21/2022] Open
Abstract
We developed a new versatile strategy that allows the detection of several classes of RNases (i.e., targeting ss- or ds-RNA, DNA/RNA hetero-hybrid or junctions) with higher sensitivity than existing assays. Our two-step approach consists of a DNA-RNA-DNA chimeric Hairpin Probe (cHP) conjugated to magnetic microparticles and containing a DNAzyme sequence in its terminal region, and molecular beacons for fluorescence signal generation. In the first step, the digestion of the RNA portion of the cHP sequences in presence of RNases leads to the release of multiple copies of the DNAzyme in solution. Then, after magnetic washing, each DNAzyme molecule elicits the catalytic cleavage of numerous molecular beacons, providing a strong amplification of the overall sensitivity of the assay. We successfully applied our approach to detect very low concentrations of RNase A, E. coli RNase I, and RNase H. Furthermore, we analyzed the effect of two antibiotics (penicillin and streptomycin) on RNase H activity, demonstrating the applicability of our strategy for the screening of inhibitors. Finally, we exploited our system to detect RNase activity directly in crude biological samples (i.e., blood and saliva) and in cell culture medium, highlighting its suitability as cheap and sensitive tool for the detection of RNase levels.
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22
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Yamashita Y, Lambein I, Kobayashi S, Onouchi H, Chiba Y, Naito S. A halt in poly(A) shortening during S-adenosyl-L-methionine-induced translation arrest in CGS1 mRNA of Arabidopsis thaliana. Genes Genet Syst 2014; 88:241-9. [PMID: 24463527 DOI: 10.1266/ggs.88.241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cystathionine γ-synthase (CGS) catalyzes the first committed step of methionine (Met) biosynthesis in plants. Expression of the Arabidopsis thaliana CGS1 gene is negatively feedback-regulated in response to the direct Met metabolite S-adenosyl-L-methionine (AdoMet). This regulation occurs at the step of mRNA stability during translation and is coupled with AdoMet-induced CGS1-specific translation arrest. In general, mRNA decay is initiated by a shortening of the poly(A) tail. However, this process has not been studied in detail in cases where regulatory events, such as programmed translation arrest, are involved. Here, we report that the poly(A) tail of the full-length CGS1 mRNA showed an apparent increase from 50-80 nucleotides (nt) to 140-150 nt after the induction of CGS1 mRNA degradation. This finding was unexpected because mRNAs that are destined for degradation harbored longer poly(A) tail than mRNAs that were not targeted for degradation. The results suggest that poly(A) shortening is inhibited or delayed during AdoMet-induced translation arrest of CGS1 mRNA. We propose an explanation for this phenomenon that remains consistent with the recent model of actively translating mRNA. We also found that CGS1 mRNA degradation intermediates, which are 5'-truncated forms of CGS1 mRNA, had a short poly(A) tail of 10-30 nt. This suggests that poly(A) shortening occurs rapidly on the degradation intermediates. The present study highlights CGS1 mRNA degradation as a useful system to understand the dynamic features of poly(A) shortening.
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Affiliation(s)
- Yui Yamashita
- Graduate School of Life Science, Hokkaido University
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23
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Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nat Chem 2014; 6:295-302. [PMID: 24651195 DOI: 10.1038/nchem.1869] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/13/2014] [Indexed: 12/12/2022]
Abstract
In vitro compartmentalization of biochemical reaction networks is a crucial step towards engineering artificial cell-scale devices and systems. At this scale the dynamics of molecular systems becomes stochastic, which introduces several engineering challenges and opportunities. Here we study a programmable transcriptional oscillator system that is compartmentalized into microemulsion droplets with volumes between 33 fl and 16 pl. Simultaneous measurement of large populations of droplets reveals major variations in the amplitude, frequency and damping of the oscillations. Variability increases for smaller droplets and depends on the operating point of the oscillator. Rather than reflecting the stochastic kinetics of the chemical reaction network itself, the variability can be attributed to the statistical variation of reactant concentrations created during their partitioning into droplets. We anticipate that robustness to partitioning variability will be a critical challenge for engineering cell-scale systems, and that highly parallel time-series acquisition from microemulsion droplets will become a key tool for characterization of stochastic circuit function.
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24
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El-Yazbi AF, Loppnow GR. Chimeric RNA–DNA Molecular Beacons for Quantification of Nucleic Acids, Single Nucleotide Polymophisms, and Nucleic Acid Damage. Anal Chem 2013; 85:4321-7. [DOI: 10.1021/ac301669y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
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25
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Leung CH, Zhong HJ, He HZ, Lu L, Chan DSH, Ma DL. Luminescent oligonucleotide-based detection of enzymes involved with DNA repair. Chem Sci 2013. [DOI: 10.1039/c3sc51228b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Liu B, Xiang D, Long Y, Tong C. Real time monitoring of junction ribonuclease activity of RNase H using chimeric molecular beacons. Analyst 2013; 138:3238-45. [DOI: 10.1039/c3an36414c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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27
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Subsoontorn P, Kim J, Winfree E. Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch. ACS Synth Biol 2012; 1:299-316. [PMID: 23651285 DOI: 10.1021/sb300018h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An overarching goal of synthetic and systems biology is to engineer and understand complex biochemical systems by rationally designing and analyzing their basic component interactions. Practically, the extent to which such reductionist approaches can be applied is unclear especially as the complexity of the system increases. Toward gradually increasing the complexity of systematically engineered systems, programmable synthetic circuits operating in cell-free in vitro environments offer a valuable testing ground for principles for the design, characterization, and analysis of complex biochemical systems. Here we illustrate this approach using in vitro transcriptional circuits ("genelets") while developing an activatable transcriptional switch motif and configuring it as a bistable autoregulatory circuit, using just four synthetic DNA strands and three essential enzymes, bacteriophage T7 RNA polymerase, Escherichia coli ribonuclease H, and ribonuclease R. Fulfilling the promise of predictable system design, the thermodynamic and kinetic constraints prescribed at the sequence level were enough to experimentally demonstrate intended bistable dynamics for the synthetic autoregulatory switch. A simple mathematical model was constructed based on the mechanistic understanding of elementary reactions, and a Monte Carlo Bayesian inference approach was employed to find parameter sets compatible with a training set of experimental results; this ensemble of parameter sets was then used to predict a test set of additional experiments with reasonable agreement and to provide a rigorous basis for confidence in the mechanistic model. Our work demonstrates that programmable in vitro biochemical circuits can serve as a testing ground for evaluating methods for the design and analysis of more complex biochemical systems such as living cells.
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Affiliation(s)
- Pakpoom Subsoontorn
- Departments of †Biology, ‡Computation and Neural Systems, §Computer Science, and ∥Bioengineering, California Institute of Technology,
Pasadena, California, 91125, United States
| | - Jongmin Kim
- Departments of †Biology, ‡Computation and Neural Systems, §Computer Science, and ∥Bioengineering, California Institute of Technology,
Pasadena, California, 91125, United States
| | - Erik Winfree
- Departments of †Biology, ‡Computation and Neural Systems, §Computer Science, and ∥Bioengineering, California Institute of Technology,
Pasadena, California, 91125, United States
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28
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Kinetic analysis of FTO (fat mass and obesity-associated) reveals that it is unlikely to function as a sensor for 2-oxoglutarate. Biochem J 2012; 444:183-7. [PMID: 22435707 DOI: 10.1042/bj20120065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Genomewide-association studies have revealed that SNPs (single nucleotide polymorphisms) in FTO (fat mass and obesity-associated) are robustly associated with BMI (body mass index) and obesity. FTO is an Fe(II) 2-OG (2-oxoglutarate)-dependent dioxygenase that can demethylate 3-meT (3-methylthymine) in single-stranded DNA, as well as 3-meU (3-methyluracil) and N6-methyl adenosine in RNA. In the present paper we describe the development of an RNase-cleavage assay measuring the demethylation activity of FTO on 3-meU. RNase A cleaves at the 3'-end of pyrimidines, including uracil, and a methyl group at position three of uracil inhibits cleavage. An oligonucleotide probe was designed consisting of a DNA stem, an RNA loop containing a single 3-meU as the only RNase A-cleavage site, a fluorescent reporter on one end and a quencher at the other end. FTO demethylation of the unique 3-meU enables RNase A cleavage, releasing the quencher and enabling a fluorescent signal. In the presence of excess RNase A, FTO activity is limiting to the development of fluorescent signal, which can be read continuously and is able to discriminate between wild-type and the catalytically dead R316Q FTO. 2-OG is a co-substrate of FTO and, as a metabolite in the citric acid cycle, is a marker of intracellular nutritional status. The assay described in the present paper was used to measure, for the first time, the K(m) of FTO for 2-OG. The K(m) of 2.88 μM is up to 10-fold lower than the estimated intracellular concentrations of 2-OG, rendering it unlikely that FTO functions as a sensor for 2-OG levels.
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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30
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Sípová H, Vaisocherová H, Stěpánek J, Homola J. A dual surface plasmon resonance assay for the determination of ribonuclease H activity. Biosens Bioelectron 2010; 26:1605-11. [PMID: 20829018 DOI: 10.1016/j.bios.2010.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/16/2010] [Accepted: 08/04/2010] [Indexed: 10/19/2022]
Abstract
There is a demand for efficient tools for the monitoring of RNase H activity. We report on a new assay which allows for simultaneous (1) real-time monitoring of RNase H activity and (2) detection of cleavage reaction products. The dual assay is implemented using a multichannel surface plasmon resonance (SPR) biosensor with two independently functionalized sensing areas in a single fluidic path. In the first sensing area the RNA cleavage by RNase H is monitored, while the products of the cleavage reaction are captured in the second sensing area with specific DNA probes. The assay was optimized with respect to AON concentration and temperature. A significant improvement was obtained with special chimeric probes, which contain RNA substrate for RNase H and a longer deoxyribonucleotide tail, which enhances the SPR signal. It has been shown that RNase H stabilizes the RNA:DNA hybrid duplex before the cleavage. The potential of the assay is demonstrated in the study in which the ability of natural and modified oligonucleotides to activate RNase H is examined.
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Affiliation(s)
- Hana Sípová
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, 182 51 Prague, Czech Republic
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31
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Hu D, Pu F, Huang Z, Ren J, Qu X. A Quadruplex-Based, Label-Free, and Real-Time Fluorescence Assay for RNase H Activity and Inhibition. Chemistry 2010; 16:2605-10. [DOI: 10.1002/chem.200902166] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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Hartl MJ, Mayr F, Rethwilm A, Wöhrl BM. Biophysical and enzymatic properties of the simian and prototype foamy virus reverse transcriptases. Retrovirology 2010; 7:5. [PMID: 20113504 PMCID: PMC2835651 DOI: 10.1186/1742-4690-7-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/29/2010] [Indexed: 11/28/2022] Open
Abstract
Background The foamy virus Pol protein is translated independently from Gag using a separate mRNA. Thus, in contrast to orthoretroviruses no Gag-Pol precursor protein is synthesized. Only the integrase domain is cleaved off from Pol resulting in a mature reverse transcriptase harboring the protease domain at the N-terminus (PR-RT). Although the homology between the PR-RTs from simian foamy virus from macaques (SFVmac) and the prototype foamy virus (PFV), probably originating from chimpanzee, exceeds 90%, several differences in the biophysical and biochemical properties of the two enzymes have been reported (i.e. SFVmac develops resistance to the nucleoside inhibitor azidothymidine (AZT) whereas PFV remains AZT sensitive even if the resistance mutations from SFVmac PR-RT are introduced into the PFV PR-RT gene). Moreover, contradictory data on the monomer/dimer status of the foamy virus protease have been published. Results We set out to purify and directly compare the monomer/dimer status and the enzymatic behavior of the two wild type PR-RT enzymes from SFVmac and PFV in order to get a better understanding of the protein and enzyme functions. We determined kinetic parameters for the two enzymes, and we show that PFV PR-RT is also a monomeric protein. Conclusions Our data show that the PR-RTs from SFV and PFV are monomeric proteins with similar biochemical and biophysical properties that are in some aspects comparable with MLV RT, but differ from those of HIV-1 RT. These differences might be due to the different conditions the viruses are confronted with in dividing and non-dividing cells.
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Affiliation(s)
- Maximilian J Hartl
- Universität Bayreuth, Lehrstuhl für Struktur und Chemie der Biopolymere & Research, Center for Biomacromolecules, 95440 Bayreuth, Germany
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33
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Wahba AS, Esmaeili A, Damha MJ, Hudson RHE. A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity. Nucleic Acids Res 2010; 38:1048-56. [PMID: 19933258 PMCID: PMC2817455 DOI: 10.1093/nar/gkp1022] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 10/19/2009] [Accepted: 10/19/2009] [Indexed: 12/12/2022] Open
Abstract
6-Phenylpyrrolocytidine (PhpC), a structurally conservative and highly fluorescent cytidine analog, was incorporated into oligoribonucleotides. The PhpC-containing RNA formed native-like duplex structures with complementary DNA or RNA. The PhpC-modification was found to act as a sensitive reporter group being non-disruptive to structure and the enzymatic activity of RNase H. A RNA/DNA hybrid possessing a single PhpC insert was an excellent substrate for HIV-1 RT Ribonuclease H and rapidly reported cleavage of the RNA strand with a 14-fold increase in fluorescence intensity. The PhpC-based assay for RNase H was superior to the traditional molecular beacon approach in terms of responsiveness, rapidity and ease (single label versus dual). Furthermore, the PhpC-based assay is amenable to high-throughput microplate assay format and may form the basis for a new screen for inhibitors of HIV-RT RNase H.
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Affiliation(s)
- Alexander S. Wahba
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
| | - Abbasali Esmaeili
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
| | - Robert H. E. Hudson
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
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34
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Garafutdinov RR, Nikonorov IM, Chemeris DA, Postrigan' BN, Chubukova OV, Talipov RF, Vakhitov VA, Chemeris AV. [New approaches to the real-time detection of nucleotide mismatches by means of chimeric hybridization probes]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:665-73. [PMID: 19915645 DOI: 10.1134/s1068162009050100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
New approaches to the detection of impaired nucleotides based on the allele specific ligation of a "C probe" followed by rolling circle amplification have been developed. The detection of amplification products was realized by using enzymatic and deoxyribozyme digestion of fluorescently-labeled DNA-RNA-DNA chimeric oligonucleotide structures in cycling probe technology (CPT) in real-time mode.
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Affiliation(s)
- R R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia.
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35
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Liu L, Li X, Hou S, Xue Y, Yao Y, Ma Y, Feng X, He S, Lu Y, Wang Y, Zeng X. Nanoparticles from block copolymer encapsulating Re(phen) complexes as bifunctional agents for cell imaging and gene transfection. Chem Commun (Camb) 2009:6759-61. [DOI: 10.1039/b912659g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Zhang Y, Li Z, Cheng Y, Lv X. Colorimetric detection of microRNA and RNase H activity in homogeneous solution with cationic polythiophene derivative. Chem Commun (Camb) 2009:3172-4. [DOI: 10.1039/b904579a] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Chen Y, Yang CJ, Wu Y, Conlon P, Kim Y, Lin H, Tan W. Light-Switching Excimer Beacon Assays For Ribonuclease H Kinetic Study. Chembiochem 2008; 9:355-9. [DOI: 10.1002/cbic.200700542] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Seferos DS, Giljohann DA, Hill HD, Prigodich AE, Mirkin CA. Nano-flares: probes for transfection and mRNA detection in living cells. J Am Chem Soc 2007; 129:15477-9. [PMID: 18034495 DOI: 10.1021/ja0776529] [Citation(s) in RCA: 535] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dwight S Seferos
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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39
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Wood RJ, Maynard-Smith MD, Robinson VL, Oyston PC, Titball RW, Roach PL. Kinetic analysis of Yersinia pestis DNA adenine methyltransferase activity using a hemimethylated molecular break light oligonucleotide. PLoS One 2007; 2:e801. [PMID: 17726531 PMCID: PMC1949145 DOI: 10.1371/journal.pone.0000801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 08/05/2007] [Indexed: 11/19/2022] Open
Abstract
Background DNA adenine methylation plays an important role in several critical bacterial processes including mismatch repair, the timing of DNA replication and the transcriptional control of gene expression. The dependence of bacterial virulence on DNA adenine methyltransferase (Dam) has led to the proposal that selective Dam inhibitors might function as broad spectrum antibiotics. Methodology/Principal Findings Herein we report the expression and purification of Yersinia pestis Dam and the development of a continuous fluorescence based assay for DNA adenine methyltransferase activity that is suitable for determining the kinetic parameters of the enzyme and for high throughput screening against potential Dam inhibitors. The assay utilised a hemimethylated break light oligonucleotide substrate containing a GATC methylation site. When this substrate was fully methylated by Dam, it became a substrate for the restriction enzyme DpnI, resulting in separation of fluorophore (fluorescein) and quencher (dabcyl) and therefore an increase in fluorescence. The assays were monitored in real time using a fluorescence microplate reader in 96 well format and were used for the kinetic characterisation of Yersinia pestis Dam, its substrates and the known Dam inhibitor, S-adenosylhomocysteine. The assay has been validated for high throughput screening, giving a Z-factor of 0.71±0.07 indicating that it is a sensitive assay for the identification of inhibitors. Conclusions/Significance The assay is therefore suitable for high throughput screening for inhibitors of DNA adenine methyltransferases and the kinetic characterisation of the inhibition.
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Affiliation(s)
- Robert J. Wood
- School of Chemistry, University of Southampton, Southampton, United Kingdom
- * To whom correspondence should be addressed. E-mail: (RW); (PR)
| | | | - Victoria L. Robinson
- Chemical and Biological Sciences, Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | - Petra C.F. Oyston
- Chemical and Biological Sciences, Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | - Rick W. Titball
- Chemical and Biological Sciences, Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | - Peter L. Roach
- School of Chemistry, University of Southampton, Southampton, United Kingdom
- * To whom correspondence should be addressed. E-mail: (RW); (PR)
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40
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Kim J, White KS, Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol 2006; 2:68. [PMID: 17170763 PMCID: PMC1762086 DOI: 10.1038/msb4100099] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 08/30/2006] [Indexed: 11/09/2022] Open
Abstract
Information processing using biochemical circuits is essential for survival and reproduction of natural organisms. As stripped-down analogs of genetic regulatory networks in cells, we engineered artificial transcriptional networks consisting of synthetic DNA switches, regulated by RNA signals acting as transcription repressors, and two enzymes, bacteriophage T7 RNA polymerase and Escherichia coli ribonuclease H. The synthetic switch design is modular with programmable connectivity and allows dynamic control of RNA signals through enzyme-mediated production and degradation. The switches support sharp and adjustable thresholds using a competitive hybridization mechanism, allowing arbitrary analog or digital circuits to be created in principle. As an example, we constructed an in vitro bistable memory by wiring together two synthetic switches and performed a systematic quantitative characterization. Good agreement between experimental data and a simple mathematical model was obtained for switch input/output functions, phase plane trajectories, and the bifurcation diagram for bistability. Construction of larger synthetic circuits provides a unique opportunity for evaluating model inference, prediction, and design of complex biochemical systems and could be used to control nanoscale devices and artificial cells.
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Affiliation(s)
- Jongmin Kim
- Biology, California Institute of Technology, Pasadena, CA, USA
| | - Kristin S White
- Computer Science, California Institute of Technology, Pasadena, CA, USA
| | - Erik Winfree
- Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA
- Computer Science, California Institute of Technology, Pasadena, CA, USA
- Computer Science and Computation & Neural Systems, California Institute of Technology, M/S 136-93, 1200 E California Blvd, Pasadena, CA 91125, USA. Tel.: +1 626 395 6246; Fax: +1 626 584 0630;
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41
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Potenza N, Salvatore V, Migliozzi A, Martone V, Nobile V, Russo A. Hybridase activity of human ribonuclease-1 revealed by a real-time fluorometric assay. Nucleic Acids Res 2006; 34:2906-13. [PMID: 16738129 PMCID: PMC1474055 DOI: 10.1093/nar/gkl368] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Human ribonuclease-1 (hRNase-1) is an extracellular enzyme found in exocrine pancreas, blood, milk, saliva, urine and seminal plasma, which has been implicated in digestion of dietary RNA and in antiviral host defense. The enzyme is characterized by a high catalytic activity toward both single-stranded and double-stranded RNA. In this study, we explored the possibility that hRNase-1 may also be provided with a ribonuclease H activity, i.e. be able to digest the RNA component of RNA:DNA hybrids. For this purpose, we developed an accurate and sensitive real-time RNase H assay based on a fluorogenic substrate made of a 12 nt 5′-fluorescein-labeled RNA hybridized to a complementary 3′-quencher-modified DNA. Under physiological-like conditions, hRNase-1 was found to cleave the RNA:DNA hybrid very efficiently, as expressed by a kcat/Km of 330 000 M−1 s−1, a value that is over 180-fold higher than that obtained with the homologous bovine RNase A and only 8-fold lower than that measured with Escherichia coli RNase H. The kinetic characterization of hRNase-1 showed that its hybridase activity is maximal at neutral pH, increases with lowering ionic strength and is fully inhibited by the cytosolic RNase inhibitor. Overall, the reported data widen our knowledge of the enzymatic properties of hRNase-1 and provide new elements for the comprehension of its biological function.
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Affiliation(s)
| | | | | | | | | | - Aniello Russo
- To whom correspondence should be addressed. Tel: +39 0823 274569; Fax: +39 0823 274571;
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Potenza N, De Colibus L, Russo A. Gel-based assay for ribonuclease H activity toward unlabeled poly(A)-poly(dT). Anal Biochem 2005; 337:167-9. [PMID: 15649392 DOI: 10.1016/j.ab.2004.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Indexed: 10/26/2022]
Affiliation(s)
- Nicoletta Potenza
- Department of Life Sciences, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
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43
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Peng XH, Cao ZH, Xia JT, Carlson GW, Lewis MM, Wood WC, Yang L. Real-time detection of gene expression in cancer cells using molecular beacon imaging: new strategies for cancer research. Cancer Res 2005; 65:1909-17. [PMID: 15753390 DOI: 10.1158/0008-5472.can-04-3196] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Development of novel approaches for quantitative analysis of gene expression in intact tumor cells should provide new means for cancer detection and for studying the response of cancer cells to biological and therapeutic reagents. We developed procedures for detecting the levels of expression of multiple genes in fixed as well as viable cells using molecular beacon imaging technology. We found that simultaneous delivery of molecular beacons targeting survivin and cyclin D1 mRNAs produced strong fluorescence in breast cancer but not in normal breast cells. Importantly, fluorescence intensity correlated well with the level of gene expression in the cells detected by real-time reverse transcription-PCR or Western blot analysis. We further show that molecular beacons can detect changes of survivin gene expression in viable cancer cells following epidermal growth factor stimulation, docetaxel treatment, and overexpression of p53 gene. Thus, molecular beacon imaging is a simple and specific method for detecting gene expression in cancer cells. It has great potential for cancer detection and drug development.
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Affiliation(s)
- Xiang-Hong Peng
- Department of Surgery, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Maksimenko A, Ishchenko AA, Sanz G, Laval J, Elder RH, Saparbaev MK. A molecular beacon assay for measuring base excision repair activities. Biochem Biophys Res Commun 2004; 319:240-6. [PMID: 15158468 DOI: 10.1016/j.bbrc.2004.04.179] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2004] [Indexed: 11/17/2022]
Abstract
The base excision repair (BER) pathway plays a key role in protecting the genome from endogenous DNA damage. Current methods to measure BER activities are indirect and cumbersome. Here, we introduce a direct method to assay DNA excision repair that is suitable for automation and industrial use, based on the fluorescence quenching mechanism of molecular beacons. We designed a single-stranded DNA oligonucleotide labelled with a 5'-fluorescein (F) and a 3'-Dabcyl (D) in which the fluorophore, F, is held in close proximity to the quencher, D, by the stem-loop structure design of the oligonucleotide. Following removal of the modified base or incision of the oligonucleotide, the fluorophore is separated from the quencher and fluorescence can be detected as a function of time. Several modified beacons have been used to validate the assay on both cell-free extracts and purified proteins. We have further developed the method to analyze BER in cultured cells. As described, the molecular beacon-based assay can be applied to all DNA modifications processed by DNA excision/incision repair pathways. Possible applications of the assay are discussed, including high-throughput real-time DNA repair measurements both in vitro and in living cells.
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Affiliation(s)
- Andrei Maksimenko
- BioAlliance Pharma SA, 59, Bvd du Général Martial Valin, 75015 Paris, France
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45
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Powe AM, Fletcher KA, St Luce NN, Lowry M, Neal S, McCarroll ME, Oldham PB, McGown LB, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2004; 76:4614-34. [PMID: 15307770 DOI: 10.1021/ac040095d] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Aleeta M Powe
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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46
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Parniak MA, Min KL, Budihas SR, Le Grice SFJ, Beutler JA. A fluorescence-based high-throughput screening assay for inhibitors of human immunodeficiency virus-1 reverse transcriptase-associated ribonuclease H activity. Anal Biochem 2004; 322:33-9. [PMID: 14705777 DOI: 10.1016/j.ab.2003.06.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2003] [Indexed: 11/18/2022]
Abstract
A fluorescence resonance energy transfer assay readily applicable to 96-well and 384-well microplate formats with robotic operation was developed to enable high-throughput screening for inhibitors of human immunodeficiency virus-1 (HIV-1) reverse transcriptase (RT)-associated RNase H activity, an underexplored target for antiretroviral development. The assay substrate is an 18-nucleotide 3'-fluorescein-labeled RNA annealed to a complementary 18-nucleotide 5'-Dabcyl-modified DNA. The intact duplex has an extremely low background fluorescent signal and provides up to 50-fold fluorescent signal enhancement following hydrolysis. The size and sequence of the duplex are such that HIV-1 RT-RNase H cuts the RNA strand close to the 3' end. The fluorescein-labeled ribonucleotide fragment readily dissociates from the complementary DNA at room temperature with immediate generation of a fluorescent signal. This assay is rapid, inexpensive, and robust, providing Z' factors of 0.8 and coefficients of variation of about 5%. The assay can be carried out both in real-time (continuous) and in "quench" modes; the latter requires only two addition steps with no washing and is thus suitable for robotic operation. Several chemical libraries totaling more than 106,000 compounds were screened with this assay in approximately 1 month.
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Affiliation(s)
- Michael A Parniak
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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47
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McKillip JL, Drake M. Real-time nucleic acid-based detection methods for pathogenic bacteria in food. J Food Prot 2004; 67:823-32. [PMID: 15083739 DOI: 10.4315/0362-028x-67.4.823] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Quality assurance in the food industry in recent years has involved the acceptance and implementation of a variety of nucleic acid-based methods for rapid and sensitive detection of food-associated pathogenic bacteria. Techniques such as polymerase chain reaction have greatly expedited the process of pathogen detection and have in some cases replaced traditional methods for bacterial enumeration in food. Conventional PCR, albeit sensitive and specific under optimized conditions, obligates the user to employ agarose gel electrophoresis as the means for endpoint analysis following sample processing. For the last few years, a variety of real-time PCR chemistries and detection instruments have appeared on the market, and many of these lend themselves to applications in food microbiology. These approaches afford a user the ability to amplify DNA or RNA, as well as detect and confirm target sequence identity in a closed-tube format with the use of a variety of fluorophores, labeled probes, or both, without the need to run gels. Such real-time chemistries also offer greater sensitivity than traditional gel visualization and can be semiquantitative and multiplexed depending on the specific experimental objectives. This review emphasizes the current systems available for real-time PCR-based pathogen detection, the basic mechanisms and requirements for each, and the prospects for development over the next few years in the food industry.
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Affiliation(s)
- John L McKillip
- Department of Biology, Ball State University, Muncie, Indiana 47306, USA
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48
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Gros L, Maksimenko AV, Privezentzev CV, Laval J, Saparbaev MK. Hijacking of the human alkyl-N-purine-DNA glycosylase by 3,N4-ethenocytosine, a lipid peroxidation-induced DNA adduct. J Biol Chem 2004; 279:17723-30. [PMID: 14761949 DOI: 10.1074/jbc.m314010200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipid peroxidation generates aldehydes, which react with DNA bases, forming genotoxic exocyclic etheno(epsilon)-adducts. E-bases have been implicated in vinyl chloride-induced carcinogenesis, and increased levels of these DNA lesions formed by endogenous processes are found in human degenerative disorders. E-adducts are repaired by the base excision repair pathway. Here, we report the efficient biological hijacking of the human alkyl-N-purine-DNA glycosylase (ANPG) by 3,N(4)-ethenocytosine (epsilonC) when present in DNA. Unlike the ethenopurines, ANPG does not excise, but binds to epsilonC when present in either double-stranded or single-stranded DNA. We developed a direct assay, based on the fluorescence quenching mechanism of molecular beacons, to measure a DNA glycosylase activity. Molecular beacons containing modified residues have been used to demonstrate that the epsilonC.ANPG interaction inhibits excision repair both in reconstituted systems and in cultured human cells. Furthermore, we show that the epsilonC.ANPG complex blocks primer extension by the Klenow fragment of DNA polymerase I. These results suggest that epsilonC could be more genotoxic than 1,N(6)-ethenoadenine (epsilonA) residues in vivo. The proposed model of ANPG-mediated genotoxicity of epsilonC provides a new insight in the molecular basis of lipid peroxidation-induced cell death and genome instability in cancer.
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Affiliation(s)
- Laurent Gros
- Groupe "Réparation de l'ADN," CNRS Unité Mixte de Recherche 8113/LBPA-ENS Cachan, Institut Gustave Roussy, 39, rue Camille Desmoulins, 94805 Villejuif Cedex, France
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