1
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Tramontano E, Corona A, Menéndez-Arias L. Ribonuclease H, an unexploited target for antiviral intervention against HIV and hepatitis B virus. Antiviral Res 2019; 171:104613. [PMID: 31550450 DOI: 10.1016/j.antiviral.2019.104613] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/18/2022]
Abstract
Ribonucleases H (RNases H) are endonucleolytic enzymes, evolutionarily related to retroviral integrases, DNA transposases, resolvases and numerous nucleases. RNases H cleave RNA in RNA/DNA hybrids and their activity plays an important role in the replication of prokaryotic and eukaryotic genomes, as well as in the replication of reverse-transcribing viruses. During reverse transcription, the RNase H activity of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) degrades the viral genomic RNA to facilitate the synthesis of viral double-stranded DNA. HIV and HBV reverse transcriptases contain DNA polymerase and RNase H domains that act in a coordinated manner to produce double-stranded viral DNA. Although RNase H inhibitors have not been developed into licensed drugs, recent progress has led to the identification of a number of small molecules with inhibitory activity at low micromolar or even nanomolar concentrations. These compounds can be classified into metal-chelating active site inhibitors and allosteric inhibitors. Among them, α-hydroxytropolones, N-hydroxyisoquinolinediones and N-hydroxypyridinediones represent chemotypes active against both HIV and HBV RNases H. In this review we summarize recent developments in the field including the identification of novel RNase H inhibitors, compounds with dual inhibitory activity, broad specificity and efforts to decrease their toxicity.
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Affiliation(s)
- Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
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2
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Nucleic acid-based fluorescent methods for the determination of DNA repair enzyme activities: A review. Anal Chim Acta 2019; 1060:30-44. [DOI: 10.1016/j.aca.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022]
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3
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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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4
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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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5
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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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6
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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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7
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Long KR, Lomonosova E, Li Q, Ponzar NL, Villa JA, Touchette E, Rapp S, Liley RM, Murelli RP, Grigoryan A, Buller RM, Wilson L, Bial J, Sagartz JE, Tavis JE. Efficacy of hepatitis B virus ribonuclease H inhibitors, a new class of replication antagonists, in FRG human liver chimeric mice. Antiviral Res 2018; 149:41-47. [PMID: 29129708 PMCID: PMC5743599 DOI: 10.1016/j.antiviral.2017.11.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/11/2017] [Accepted: 11/07/2017] [Indexed: 12/20/2022]
Abstract
Chronic hepatitis B virus infection cannot be cured by current therapies, so new treatments are urgently needed. We recently identified novel inhibitors of the hepatitis B virus ribonuclease H that suppress viral replication in cell culture. Here, we employed immunodeficient FRG KO mice whose livers had been engrafted with primary human hepatocytes to ask whether ribonuclease H inhibitors can suppress hepatitis B virus replication in vivo. Humanized FRG KO mice infected with hepatitis B virus were treated for two weeks with the ribonuclease H inhibitors #110, an α-hydroxytropolone, and #208, an N-hydroxypyridinedione. Hepatitis B virus viral titers and S and e antigen plasma levels were measured. Treatment with #110 and #208 caused significant reductions in plasma viremia without affecting hepatitis B virus S or e antigen levels, and viral titers rebounded following treatment cessation. This is the expected pattern for inhibitors of viral DNA synthesis. Compound #208 suppressed viral titers of both hepatitis B virus genotype A and C isolates. These data indicate that Hepatitis B virus replication can be suppressed during infection in an animal by inhibiting the viral ribonuclease H, validating the ribonuclease H as a novel target for antiviral drug development.
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Affiliation(s)
- Kelly R Long
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - Elena Lomonosova
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Qilan Li
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Nathan L Ponzar
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Juan A Villa
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Erin Touchette
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - Stephen Rapp
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - R Matt Liley
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - Ryan P Murelli
- Brookyln College & PhD Program in Chemistry at the Graduate Center of the City University of New York, NY 11210, USA.
| | - Alexandre Grigoryan
- Brookyln College & PhD Program in Chemistry at the Graduate Center of the City University of New York, NY 11210, USA.
| | - R Mark Buller
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| | - Lisa Wilson
- Yecuris Corporation, P.O. Box 4645, Tualatin, OR 97062, USA.
| | - John Bial
- Yecuris Corporation, P.O. Box 4645, Tualatin, OR 97062, USA.
| | - John E Sagartz
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - John E Tavis
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
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8
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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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9
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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10
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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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11
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Weyel XMM, Fichte MAH, Heckel A. A Two-Photon-Photocleavable Linker for Triggering Light-Induced Strand Breaks in Oligonucleotides. ACS Chem Biol 2017; 12:2183-2190. [PMID: 28678467 DOI: 10.1021/acschembio.7b00367] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We synthesized a two-photon-sensitive photocleavable linker based on the 7-diethylaminocoumarin structure and introduced it successfully into DNA strands. First, we demonstrated the inducibility of strand scissions upon irradiation at 365 nm. To verify and visualize the two-photon activity, we used a fluorescence assay based on a DNA strand displacement immobilized in a hydrogel. Additionally, we investigated its use in a new class of DNA decoys that are able to catch and release nuclear factor κB (NF-κB) by using light as an external trigger signal. In cell culture we were able to show the regulation of NF-κB-controlled transcription of green fluorescent protein.
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Affiliation(s)
- Xenia M M Weyel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Manuela A H Fichte
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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12
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Edwards TC, Lomonosova E, Patel JA, Li Q, Villa JA, Gupta AK, Morrison LA, Bailly F, Cotelle P, Giannakopoulou E, Zoidis G, Tavis JE. Inhibition of hepatitis B virus replication by N-hydroxyisoquinolinediones and related polyoxygenated heterocycles. Antiviral Res 2017; 143:205-217. [PMID: 28450058 DOI: 10.1016/j.antiviral.2017.04.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/06/2017] [Accepted: 04/22/2017] [Indexed: 12/16/2022]
Abstract
We previously reported low sensitivity of the hepatitis B virus (HBV) ribonuclease H (RNaseH) enzyme to inhibition by N-hydroxyisoquinolinedione (HID) compounds. Subsequently, our biochemical RNaseH assay was found to have a high false negative rate for predicting HBV replication inhibition, leading to underestimation of the number of HIDs that inhibit HBV replication. Here, 39 HID compounds and structurally related polyoxygenated heterocycles (POH), N-hydroxypyridinediones (HPD), and flutimides were screened for inhibition of HBV replication in vitro. Inhibiting the HBV RNaseH preferentially blocks synthesis of the positive-polarity DNA strand and causes accumulation of RNA:DNA heteroduplexes. Eleven HIDs and one HPD preferentially inhibited HBV positive-polarity DNA strand accumulation. EC50s ranged from 0.69 μM to 19 μM with therapeutic indices from 2.4 to 71. Neither the HIDs nor the HPD had an effect on the ability of the polymerase to elongate DNA strands in capsids. HBV RNaseH inhibition by the HIDs was confirmed with an improved RNaseH assay and by detecting accumulation RNA:DNA heteroduplexes in HBV capsids from cells treated with a representative HID. Therefore, the HID scaffold is more promising for anti-HBV drug discovery than we originally reported, and the HPD scaffold may hold potential for antiviral development. The preliminary structure-activity relationship will guide optimization of the HID/HPDs as HBV inhibitors.
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Affiliation(s)
- Tiffany C Edwards
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Elena Lomonosova
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Jenny A Patel
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Qilan Li
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Juan A Villa
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Ankit K Gupta
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Lynda A Morrison
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Fabrice Bailly
- University of Lille, INSERM, UMR-S 1172, Jean-Pierre Aubert Research Center, Lille, France.
| | - Philippe Cotelle
- University of Lille, INSERM, UMR-S 1172, Jean-Pierre Aubert Research Center, Lille, France.
| | - Erofili Giannakopoulou
- School of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - Grigoris Zoidis
- School of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - John E Tavis
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
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13
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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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14
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Zeng S, Huang H, Huang Y, Liu X, Qin J, Zhao S, Chen ZF, Liang H. Label-free and amplified colorimetric assay of ribonuclease H activity and inhibition based on a novel enzyme-responsive DNAzyme cascade. RSC Adv 2015. [DOI: 10.1039/c5ra05712d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A simple, label-free and amplified colorimetric assay strategy based on a novel enzyme-responsive DNAzyme cascade is developed for assay of ribonuclease H activity and inhibition. This assay exhibits high sensitivity and selectivity.
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Affiliation(s)
- Shulan Zeng
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
| | - Huakui Huang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Yong Huang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Xiaoqian Liu
- College of Chemistry and Pharmacy
- Guangxi Normal University
- Guilin
- China
| | - Jian Qin
- College of Chemistry and Pharmacy
- Guangxi Normal University
- Guilin
- China
| | - Shulin Zhao
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
| | - Zhen-Feng Chen
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
| | - Hong Liang
- Ministry of Education Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- Guangxi Normal University
- Guilin
- China
- College of Chemistry and Pharmacy
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15
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Huang J, Yang X, He X, Wang K, Liu J, Shi H, Wang Q, Guo Q, He D. Design and bioanalytical applications of DNA hairpin-based fluorescent probes. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.08.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Wu X, Chen J, Zhao JX. Ultrasensitive detection of 3′-5′ exonuclease enzymatic activity using molecular beacons. Analyst 2014; 139:1081-7. [DOI: 10.1039/c3an02040a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An ultrasensitive and rapid fluorescence assay was developed for the detection of 3′-5′ exonuclease activity using molecular beacons.
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Affiliation(s)
- Xu Wu
- Department of Chemistry
- University of North Dakota
- Grand Forks, USA
| | - Jiao Chen
- Department of Chemistry
- University of North Dakota
- Grand Forks, USA
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Abstract
Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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Ma DL, He HZ, Leung KH, Zhong HJ, Chan DSH, Leung CH. Label-free luminescent oligonucleotide-based probes. Chem Soc Rev 2013; 42:3427-40. [PMID: 23348604 DOI: 10.1039/c2cs35472a] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Breakthrough advances in chemistry and biology over the last two decades have vastly expanded the repertoire of nucleic acid structure and function with potential application in multiple areas of science and technology, including sensing and analytical applications. DNA oligonucleotides represent popular tools for the development of sensing platforms due to their low cost, rich structural polymorphism, and their ability to bind to cognate ligands with sensitivity and specificity rivaling those for protein enzymes and antibodies. In this review, we give an overview of the "label-free" approach that has been a particular focus of our group and others for the construction of luminescent DNA-based sensing platforms. The label-free strategy aims to overcome some of the drawbacks associated with the use of covalently-labeled oligonucleotides prevalent in electrochemical and optical platforms. Label-free DNA-based probes harness the selective interaction between luminescent dyes and functional oligonucleotides that exhibit a "structure-switching" response upon binding to analytes. Based on the numerous examples of label-free luminescent DNA-based probes reported recently, we envisage that this field would continue to thrive and mature in the years to come.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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19
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Jacroux T, Rieck DC, Cui R, Ouyang Y, Dong WJ. Enzymatic amplification of DNA/RNA hybrid molecular beacon signaling in nucleic acid detection. Anal Biochem 2013; 432:106-14. [PMID: 23000602 PMCID: PMC3522425 DOI: 10.1016/j.ab.2012.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 11/22/2022]
Abstract
A rapid assay operable under isothermal or nonisothermal conditions is described, where the sensitivity of a typical molecular beacon (MB) system is improved by using thermostable RNase H to enzymatically cleave an MB composed of a DNA stem and an RNA loop (R/D-MB). On hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7× above background) due to an opening of the probe and a concomitant reduction in the Förster resonance energy transfer efficiency. The addition of thermostable RNase H resulted in the cleavage of the RNA loop, which eliminated energy transfer. The cleavage step also released bound target DNA, enabling it to bind to another R/D-MB probe and rendering the approach a cyclic amplification scheme. Full processing of R/D-MBs maximized the fluorescence signal to the fullest extent possible (12.9× above background), resulting in an approximately 2- to 2.8-fold increase in the signal-to-noise ratio observed isothermally at 50 °C following the addition of RNase H. The probe was also used to monitor real-time polymerase chain reactions by measuring enhancement of donor fluorescence on R/D-MB binding to amplified pUC19 template dilutions. Hence, the R/D-MB-RNase H scheme can be applied to a broad range of nucleic acid amplification methods.
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Affiliation(s)
- Thomas Jacroux
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Daniel C. Rieck
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Rong Cui
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
| | - Yexin Ouyang
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
| | - Wen-Ji Dong
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
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20
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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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21
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Maity A, Das S, Mandal S, Gupta P, Purkayastha P. Interaction of semicarbazide and thiosemicarbazide pyrene derivatives with anionic and cationic micelles: changed character of pyrene due to alteration in charge density induced by the side chains. RSC Adv 2013. [DOI: 10.1039/c3ra41029c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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22
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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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23
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Deng J, Jin Y, Chen G, Wang L. Label-free fluorescent assay for real-time monitoring site-specific DNA cleavage by EcoRI endonuclease. Analyst 2012; 137:1713-7. [PMID: 22354164 DOI: 10.1039/c2an16287c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA cleavage reaction catalyzed by nucleases is essential in many important biological processes and medicinal chemistry. Therefore, it is important to develop reliable and facile methods to assay nuclease activity. With this goal in mind, we report a fluorescent assay for label-free, facile, and real-time monitoring of DNA cleavage by EcoRI endonuclease using SYBR Green I (SGI) as a signal probe. The fluorescence of SGI dramatically increased when the free SGI was mixed with double-stranded DNA (dsDNA) substrate. Upon interacting with EcoRI, which cleaves the dsDNA into small fragments, the weakened interaction between SGI and the shortened DNA fragments caused a decrease in fluorescence of SGI. EcoRI-DNA interaction was real-time studied by monitoring fluorescence change with the prolonging of interaction time. The important kinetic parameters, including Michaelis-Menten constant (K(M)) and maximum initial velocity (V(max)), were accurately calculated, which is consistent with previously reported studies. Site-specific DNA cleavage by EcoRI endonuclease has also been verified by gel electrophoresis analysis, which indicated that this method is a simple and effective approach to assay DNA cleavage reaction. Specificity investigation demonstrated that EcoRI-DNA interactions can be studied with high selectivity. Compared with previously reported methods, this approach is selective, simple, convenient and cost-efficient without any labeling of the probe or of the target.
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Affiliation(s)
- Jing Deng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemistry Engineering, Shaanxi Normal University, Xi'an, 710062, China
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24
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Yin BC, You M, Tan W, Ye BC. Mercury(II) ion detection via pyrene-mediated photolysis of disulfide bonds. Chemistry 2012; 18:1286-9. [PMID: 22223216 DOI: 10.1002/chem.201103348] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/12/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Bin-Cheng Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, P.R. China
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25
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Huang K, Martí AA. Recent trends in molecular beacon design and applications. Anal Bioanal Chem 2011; 402:3091-102. [PMID: 22159461 DOI: 10.1007/s00216-011-5570-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/26/2022]
Abstract
A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.
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Affiliation(s)
- Kewei Huang
- Department of Chemistry, Rice University, 6100 South Main Street, Houston, TX 77005, USA
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26
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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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27
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Menacher F, Wagenknecht HA. Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution. Photochem Photobiol Sci 2011; 10:1275-8. [PMID: 21547330 DOI: 10.1039/c1pp05091e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular beacons with an excitonically interacting perylene bisimide base pair show the presence of the complementary olignucleotide sequence by both absorption and fluorescence changes.
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Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany
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28
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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29
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Huang J, Wu Y, Chen Y, Zhu Z, Yang X, Yang CJ, Wang K, Tan W. Pyrene-Excimer Probes Based on the Hybridization Chain Reaction for the Detection of Nucleic Acids in Complex Biological Fluids. Angew Chem Int Ed Engl 2010; 50:401-4. [DOI: 10.1002/anie.201005375] [Citation(s) in RCA: 469] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Huang J, Wu Y, Chen Y, Zhu Z, Yang X, Yang CJ, Wang K, Tan W. Pyrene-Excimer Probes Based on the Hybridization Chain Reaction for the Detection of Nucleic Acids in Complex Biological Fluids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005375] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Huang J, Zhu Z, Bamrungsap S, Zhu G, You M, He X, Wang K, Tan W. Competition-mediated pyrene-switching aptasensor: probing lysozyme in human serum with a monomer-excimer fluorescence switch. Anal Chem 2010; 82:10158-63. [PMID: 21080638 DOI: 10.1021/ac102277p] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysozyme (Lys) plays crucial roles in the innate immune system, and the detection of Lys in urine and serum has considerable clinical importance. Traditionally, the presence of Lys has been detected by immunoassays; however, these assays are limited by the availability of commercial antibodies and tedious protein modification and prior sample purification. To address these limitations, we report here the design, synthesis, and application of a competition-mediated pyrene-switching aptasensor for selective detection of Lys in buffer and human serum. The detection strategy is based on the attachment of pyrene molecules to both ends of a hairpin DNA strand, which becomes the partially complementary competitor to an anti-Lys aptamer. In the presence of target Lys, the aptamer hybridizes with part of the competitor, which opens the hairpin such that both pyrene molecules are spatially separated. In the presence of target Lys, however, the competitor is displaced from the aptamer by the target, subsequently forming an initial hairpin structure. This brings the two pyrene moieties into close proximity to generate an excimer, which, in turn, results in a shift of fluorescence emission from ca. 400 nm (pyrene monomer) to 495 nm (pyrene excimer). The proposed method for Lys detection showed sensitivity as low as 200 pM and high selectivity in buffer. When measured by a steady-state fluorescence spectrum, the detection of Lys in human serum showed a strong fluorescent background, which obscured detection of the excimer signal. However, time-resolved emission measurement (TREM) supported the potential of the method in complex environments with background fluorescence by demonstrating the temporal separation of probe fluorescence emission decay from the intense background signal. We have also demonstrated that the same strategy can be applied to the detection of small biomolecules such as adenosine triphosphate (ATP), showing the generality of our approach. Therefore, the competition-mediated pyrene-switching aptasensor is promising to have potential for clinical and forensic applications.
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Affiliation(s)
- Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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32
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Abstract
Telomeric repeat-containing RNA (referred to as TERRA), a noncoding RNA molecule, has recently been found in mammalian cells. The detailed structural features and function of the TERRA RNA at human chromosome ends remain unclear, although this RNA molecule may be a key component of the telomere machinery. In the present studies, we investigated the structural features of human TERRA RNA in living cells. Using a light-switching pyrene probe, we found that human TERRA RNA forms a parallel G-quadruplex structure in living cells, providing the in vivo evidence for the presence of the G-quadruplex in human TERRA RNA. Furthermore, imaging experiments clearly show that TERRA RNA G-quadruplex localizes to telomere DNA at cell nuclei. These results provide valuable information to allow understanding of the structure and function of human TERRA RNA.
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33
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Kobayashi H, Ogawa M, Alford R, Choyke PL, Urano Y. New strategies for fluorescent probe design in medical diagnostic imaging. Chem Rev 2010; 110:2620-40. [PMID: 20000749 PMCID: PMC3241938 DOI: 10.1021/cr900263j] [Citation(s) in RCA: 1517] [Impact Index Per Article: 108.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hisataka Kobayashi
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892-1088, USA.
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34
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Zheng J, Li J, Gao X, Jin J, Wang K, Tan W, Yang R. Modulating Molecular Level Space Proximity: A Simple and Efficient Strategy to Design Structured DNA Probes. Anal Chem 2010; 82:3914-21. [DOI: 10.1021/ac1004713] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoxia Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianyu Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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35
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Holzhauser C, Berndl S, Menacher F, Breunig M, Göpferich A, Wagenknecht HA. Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901423] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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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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37
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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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38
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Berndl S, Wagenknecht HA. Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base. Angew Chem Int Ed Engl 2009; 48:2418-21. [PMID: 19229903 DOI: 10.1002/anie.200805981] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A fluorescent chameleon: A single thiazole orange (TO) dye, when used as an artificial DNA base shows the typical green emission, whereas the interstrand TO dimer exhibits an orange excimer-type emission inside duplex DNA (see picture).
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Affiliation(s)
- Sina Berndl
- Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
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39
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Fluoreszenz-Farbwechsel bei der DNA-Hybridisierung mit Thiazolorange als artifizieller DNA-Base. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805981] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Fujimoto K, Inouye M. [DNA duplex-based fluorescence probes/sensors using monomer-excimer switching]. YAKUGAKU ZASSHI 2008; 128:1605-13. [PMID: 18981696 DOI: 10.1248/yakushi.128.1605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this review, we report DNA duplex-based fluorescence probes/sensors using pyrene monomer-excimer switching. The review mainly comprises two topics: 1) excimer-monomer switching molecular beacons (EMS-MB) and 2) monomer-excimer switching sensors based on the structural motif of antibodies. The EMS-MBs have two pyrene fluorophores connected both at 3' and 5' ends of a single-stranded oligonucleotide. Emission switching occurs from excimer to monomer accompanying isoemissive points when the probes hybridized with target DNAs. The isoemissive points indicate the presence of only two fluorescent species, nonhybridized and hybridized probes in the mixtures, and thereby unambiguous detection of the targets is available. The probes can detect target 19-mer DNAs and can discriminate the targets from their single-nucleotide mismatches at 1 nM concentration. Furthermore, the EMS-MBs have been recently applied to kinetic study for RNase H activity by Tan et al. The structures and emission-switching properties of the EMS-MBs encourage us to develop a new class of fluorescent sensors based on the structural motif of antibodies. The sensors consist of three functional regions, benzo-15-crown-5 ether (or per-O-methylated beta-cyclodextrin), DNA, and pyrene as guest-binding, dimerizing, and sensing sites, respectively. The crown- and CD-modified sensors can detect potassium cation and porphyrin derivatives, respectively, by monomer-excimer emission switching.
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Affiliation(s)
- Kazuhisa Fujimoto
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama City, Japan.
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