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Helm J, Schöls L, Hauser S. Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases. Pharmaceutics 2022; 14:pharmaceutics14081708. [PMID: 36015334 PMCID: PMC9416334 DOI: 10.3390/pharmaceutics14081708] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are single-stranded nucleic acid strings that can be used to selectively modify protein synthesis by binding complementary (pre-)mRNA sequences. By specific arrangements of DNA and RNA into a chain of nucleic acids and additional modifications of the backbone, sugar, and base, the specificity and functionality of the designed ASOs can be adjusted. Thereby cellular uptake, toxicity, and nuclease resistance, as well as binding affinity and specificity to its target (pre-)mRNA, can be modified. Several neurodegenerative diseases are caused by autosomal dominant toxic gain-of-function mutations, which lead to toxic protein products driving disease progression. ASOs targeting such mutations—or even more comprehensively, associated variants, such as single nucleotide polymorphisms (SNPs)—promise a selective degradation of the mutant (pre-)mRNA while sparing the wild type allele. By this approach, protein expression from the wild type strand is preserved, and side effects from an unselective knockdown of both alleles can be prevented. This makes allele-specific targeting strategies a focus for future personalized therapies. Here, we provide an overview of current strategies to develop personalized, allele-specific ASO therapies for the treatment of neurodegenerative diseases, such Huntington’s disease (HD) and spinocerebellar ataxia type 3 (SCA3/MJD).
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Affiliation(s)
- Jacob Helm
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
- Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Hauser
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
- Correspondence:
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2
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Xie Y, Zhang S, Deng T, Zhang K, Ren J, Li J. A Novel DNAzyme Signal Amplification-based Colorimetric Method for RNase H Assays. ANAL SCI 2021; 37:1675-1680. [PMID: 33162413 DOI: 10.2116/analsci.20p337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A simple visual strategy was developed for the RNase H colorimetric measurement using DNAzyme-mediated signal amplification. When RNase H was presented, the RNA strand of the duplex formed by the G-rich DNA sequence (G-Rich) and its complementary RNA sequence (cp-RNA) was digested, releasing G-Rich to form HRP-mimicking DNAzymes of the G-quadruplex/hemin complexes in the presence of hemin. These DNAzymes catalyze the oxidation reaction of the substrate of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) to produce green-color products of ABTS•-, allowing for the detection of RNase H. A horseradish peroxidase (HRP)-mimicking DNAzyme of the G-quadruplex/hemin complex was used to mediate the signal amplification in the sensing strategy, resulting in high selectivity and sensitivity. This proposed colorimetric method shows a low detection limit of 0.04 U/mL, with a detection range of 0.1 to 3 U/mL. Moreover, this colorimetric method has been successfully used for RNase H assays in complicated biosamples, such as cell lysates. These results indicate that our colorimetric method not only detects RNase H in an ideal system, but also in real samples.
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Affiliation(s)
- Ye Xie
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Sina Zhang
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Ting Deng
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Ke Zhang
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Jiali Ren
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
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Abstract
Ribonucleases are useful as biomarkers and can be the source of contamination in laboratory samples, making ribonuclease detection assays important in life sciences research. With recent developments in DNA-based biosensing, several new techniques are being developed to detect ribonucleases. This review discusses some of these methods, specifically those that utilize G-quadruplex DNA structures, DNA-nanoparticle conjugates and DNA nanostructures, and the advantages and challenges associated with them.
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Sheet SK, Rabha M, Sen B, Patra SK, Aguan K, Khatua S. Ruthenium(II) Complex-Based G-quadruplex DNA Selective Luminescent 'Light-up' Probe for RNase H Activity Detection. Chembiochem 2021; 22:2880-2887. [PMID: 34314094 DOI: 10.1002/cbic.202100229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/03/2021] [Indexed: 12/14/2022]
Abstract
A bis-heteroleptic ruthenium(II) complex, 1[PF6 ]2 of benzothiazole amide substituted 2,2'-bipyridine ligand (bmbbipy) has been synthesized for the selective detection of G-quadruplex (GQ) DNA and luminescence-assay-based RNase H activity monitoring. Compound 1[PF6 ]2 exhibited aggregation-caused quenching (ACQ) in water. Aggregate formation was supported by DLS, UV-vis, and 1 H NMR spectroscopy results, and the morphology of aggregated particles was witnessed by SEM and TEM. 1[PF6 ]2 acted as an efficient GQ DNA-selective luminescent light-up probe over single-stranded and double-stranded DNA. The competency of 1[PF6 ]2 for selective GQ structure detection was established by PL and CD spectroscopy. For 1[PF6 ]2 , the PL light-up is exclusively due to the rigidification of the benzothiazole amide side arm in the presence of GQ-DNA. The interaction between the probe and GQ-DNA was analyzed by molecular docking analysis. The GQ structure detection capability of 1[PF6 ]2 was further applied in the luminescent 'off-on' RNase H activity detection. The assay utilized an RNA:DNA hybrid, obtained from 22AG2-RNA and 22AG2-DNA sequences. RNase H solely hydrolyzed the RNA of the RNA:DNA duplex and released G-rich 22AG2-DNA, which was detected via the PL enhancement of 1[PF6 ]2 . The selectivity of RNase H activity detection over various other restriction enzymes was also demonstrated.
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Affiliation(s)
- Sanjoy Kumar Sheet
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Monosh Rabha
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Bhaskar Sen
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Sumit Kumar Patra
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Kripamoy Aguan
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Snehadrinarayan Khatua
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
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5
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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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Cao Y, Ding P, Yang L, Li W, Luo Y, Wang J, Pei R. Investigation and improvement of catalytic activity of G-quadruplex/hemin DNAzymes using designed terminal G-tetrads with deoxyadenosine caps. Chem Sci 2020; 11:6896-6906. [PMID: 34094131 PMCID: PMC8159390 DOI: 10.1039/d0sc01905d] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
It is generally acknowledged that G-quadruplexes (G4s) acquire peroxidase activity upon interaction with hemin. Hemin has been demonstrated to bind selectively to the 3′-terminal G-tetrad of parallel G4s via end-stacking; however, the relationships between different terminal G-tetrads and the catalytic functions of G4/hemin DNAzymes are not fully understood. Herein, the oligonucleotide d(AGGGGA) and its three analogues, d(AGBrGBrGGA), d(AGBrGGGBrA) and d(AGBrGGBrGA) (GBr indicates 8-bromo-2′-deoxyguanosine), were designed. These oligonucleotides form three parallel G4s and one antiparallel G4 without loop regions. The scaffolds had terminal G-tetrads that were either anti-deoxyguanosines (anti-dGs) or syn-deoxyguanosines (syn-dGs) at different proportions. The results showed that the parallel G4 DNAzymes exhibited 2 to 5-fold higher peroxidase activities than the antiparallel G4 DNAzyme, which is due to the absence of the 3′-terminal G-tetrad in the antiparallel G4. Furthermore, the 3′-terminal G-tetrad consisting of four anti-dGs in parallel G4s was more energetically favorable and thus more preferable for hemin stacking compared with that consisting of four syn-dGs. We further investigated the influence of 3′ and 5′ deoxyadenosine (dA) caps on the enzymatic performance by adding 3′-3′ or 5′-5′ phosphodiester bonds to AG4A. Our data demonstrated that 3′ dA caps are versatile residues in promoting the interaction of G4s with hemin. Thus, by increasing the number of 3′ dA caps, the DNAzyme of 3′A5′-5′GG3′-3′GG5′-5′A3′ with two 5′-terminal G-tetrads can exhibit significantly high catalytic activity, which is comparable to that of 5′A3′-3′GG5′-5′GG3′-3′A5′ with two 3′-terminal G-tetrads. This study may provide insights into the catalytic mechanism of G4-based DNAzymes and strategies for promoting their catalytic activities. Investigation of the peroxidase activities of G4/hemin DNAzymes using designed terminal G-tetrads by eliminating the steric effect of loop regions.![]()
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Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
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7
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A Non-Enzyme and Non-Label Sensitive Fluorescent Aptasensor Based on Simulation-Assisted and Target-Triggered Hairpin Probe Self-Assembly for Ochratoxin a Detection. Toxins (Basel) 2020; 12:toxins12060376. [PMID: 32517279 PMCID: PMC7354513 DOI: 10.3390/toxins12060376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 01/23/2023] Open
Abstract
The monitoring and control of mycotoxins has caused widespread concern due to their adverse effects on human health. In this research, a simple, sensitive and non-label fluorescent aptasensor has been reported for mycotoxin ochratoxin A (OTA) detection based on high selectivity of aptamers and amplification of non-enzyme hybridization chain reaction (HCR). After the introduction of OTA, the aptamer portion of hairpin probe H1 will combine with OTA to form OTA-aptamer complexes. Subsequently, the remainder of the opened H1 will act as an initiator for the HCR between the two hairpin probes, causing H1 and H2 to be sequentially opened and assembled into continuous DNA duplexes embedded with numerous G-quadruplexes, leading to a significant enhancement in fluorescence signal after binding with N-methyl-mesoporphyrin IX (NMM). The proposed sensing strategy can detect OTA with concentration as low as 4.9 pM. Besides, satisfactory results have also been obtained in the tests of actual samples. More importantly, the thermodynamic properties of nucleic acid chains in the monitoring platform were analyzed and the reaction processes and conditions were simulated before carrying out biological experiments, which theoretically proved the feasibility and simplified subsequent experimental operations. Therefore, the proposed method possess a certain application value in terms of monitoring mycotoxins in food samples and improving the quality control of food security.
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8
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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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9
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Xie Y, Wang N, Li Y, Deng T, Li J, Zhang K, Yu R. Cyclodextrin supramolecular inclusion-enhanced pyrene excimer switching for highly selective detection of RNase H. Anal Chim Acta 2019; 1088:137-143. [PMID: 31623709 DOI: 10.1016/j.aca.2019.08.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/13/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
Here, we report a novel fluorescence method for the highly selective and sensitive detection of RNase H by combining the use of a dual-pyrene-labeled DNA/RNA duplex with supramolecular inclusion-enhanced fluorescence. Initially, the probe is in the "off" state due to the rigidness of the double-stranded duplex, which separates the two pyrene units. In the presence of RNase H, the RNA strand of the DNA/RNA duplex will be hydrolyzed, and the DNA strand transforms into a hairpin structure, bringing close the two pyrene units which in turn enter the hydrophobic cavity of a γ-cyclodextrin. As a result, the pyrene excimer emission is greatly enhanced, thereby realizing the detection of RNase H activity. Under optimal conditions, RNase H detection can be achieved in the range from 0.08 to 4 U/mL, with a detection limit of 0.02 U/mL.
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Affiliation(s)
- Ye Xie
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ningning Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yulong Li
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ting Deng
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Ke Zhang
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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10
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Yett A, Lin LY, Beseiso D, Miao J, Yatsunyk LA. N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA. J PORPHYR PHTHALOCYA 2019; 23:1195-1215. [PMID: 34385812 PMCID: PMC8356643 DOI: 10.1142/s1088424619300179] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.
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Affiliation(s)
- Ariana Yett
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Yingqi Lin
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Dana Beseiso
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Liliya A. Yatsunyk
- Correspondence to: Liliya A. Yatsunyk, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA. tel.: 610-328-8558,
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11
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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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12
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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13
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Thioflavin T as luminescence biosensors for nucleic acid study and RNase A activity detection. Microchem J 2019. [DOI: 10.1016/j.microc.2019.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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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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15
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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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16
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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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17
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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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18
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Yang W, Zhou X, Zhao J, Xu W. A cascade amplification strategy of catalytic hairpin assembly and hybridization chain reaction for the sensitive fluorescent assay of the model protein carcinoembryonic antigen. Mikrochim Acta 2018; 185:100. [PMID: 29594400 DOI: 10.1007/s00604-017-2620-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 12/15/2017] [Indexed: 01/21/2023]
Abstract
A cascade nucleic acid amplification strategy is presented for fluorometric aptamer based determination of the model protein carcinoembryonic antigen (CEA). Amplification is accomplished by combining catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR). In this assay, a specially designed single-stranded DNA containing the aptamer sequence (AS) specific for CEA is hybridized with an inhibitor strand (IS) to form a double-stranded DNA (IS@AS). In the presence of CEA, it will recognize and bind to the AS strand which causes the release of IS. By introducing two DNA hairpins (H1 and H2; these containing complementary sequences) CHA will be activated via the hybridization reactions of H1 and H2. This is accompanying by the formation of a double-stranded DNA (H1-H2) and the release of CEA@AS. The liberated CEA@AS further drives successive recycling of the CHA, thereby generating further copies of H1-H2. The resultant H1-H2 hybrids act as primers and trigger HCR with the help of other two DNA hairpins (H3 and H4) containing G-rich toehold at the 5'-terminus and 3'-terminus of H3 and H4, respectively. The fluorescent probe N-methyl mesoporphyrin IX (NMM) is finally intercalated into the G-rich domains of the long DNA nanostructures due to formation of G-quadruplex structures. This generates a fluorescent signal (best measured at excitation/emission wavelengths of 399/610 nm) that increases with the concentration of target (CEA). This aptamer-based fluorescence assay is highly sensitive and has a linear range that covers the 1 pg·mL-1 to 2 ng·mL-1 CEA concentration range, with a 0.3 pg·mL-1 detection limit. Graphical abstract By integrating catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) for effective signal enhancement, a novel cascade amplification strategy is presented to develop a sensitive and selective fluorescent method for the assay of the model protein carcinoembryonic antigen (CEA).
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Affiliation(s)
- Wenting Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xingxing Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, People's Republic of China
| | - Jianmin Zhao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, People's Republic of China
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, People's Republic of China.
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19
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Chen Y, Wang J, Zhang Y, Xu L, Gao T, Wang B, Pei R. Selection and characterization of a DNA aptamer to crystal violet. Photochem Photobiol Sci 2018; 17:800-806. [DOI: 10.1039/c7pp00457e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A shortened 42-mer aptamer with high affinity and good specificity for crystal violet, which showed higher fluorescence enhancement than G-quadruplexes was successfully selected.
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Affiliation(s)
- Yang Chen
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yajie Zhang
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Lijun Xu
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Tian Gao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Bing Wang
- School of Pharmacy
- Xi'an Jiaotong University
- Xi'an
- China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
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20
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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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21
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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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22
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Facile and sensitive fluorescence sensing of alkaline phosphatase activity using NMM/G-quadruplex. Talanta 2017; 172:171-175. [DOI: 10.1016/j.talanta.2017.05.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/10/2017] [Accepted: 05/14/2017] [Indexed: 11/21/2022]
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23
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Li M, Zhao A, Ren J, Qu X. N-Methyl Mesoporphyrin IX as an Effective Probe for Monitoring Alzheimer's Disease β-Amyloid Aggregation in Living Cells. ACS Chem Neurosci 2017; 8:1299-1304. [PMID: 28281745 DOI: 10.1021/acschemneuro.6b00436] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Formation of amyloid fibrils by amyloid-β peptide (Aβ) is an important step in Alzheimer's disease (AD) progression. Screening and designing of new molecules which can monitor the amyloidosis process especially in cells are diagnostically and therapeutically important. Utilizing Thioflavin T (ThT), the commonly used amyloid dye, is the most standardized way to monitor amyloid. However, with the green fluorescence emission and small Stokes shift, the fluorescence of ThT can overlap with that arising from other intrinsic fluorescent components in the cells, making it not suitable for detection of protein aggregates in vivo. Therefore, it is urgent for developing amyloid probes with large Stokes shifts and red-shifted fluorescence emission to detect Aβ aggregates in cells. In this report, we found that N-methyl mesoporphyrin IX (NMM), a widely used G-quadruplex DNA specific fluorescent binder, can be an efficient probe for monitoring Aβ fibrillation in living cells. NMM is nonfluorescent in aqueous solution or monomeric Aβ environments. However, through stacking with the Aβ assemblies, NMM emits strong fluorescence. Furthermore, the large Stokes shift and stable photoluminescence make it an ideal probe for detecting Aβ aggregates in highly fluorescent environments and cell culture. Our results provide a new sight to design and screen new reagents for monitoring the diseases associated with protein conformational disorders.
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Affiliation(s)
- Meng Li
- Laboratory of Chemical
Biology and State Key Laboratory of Rare Earth Resource Utilization,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Andong Zhao
- Laboratory of Chemical
Biology and State Key Laboratory of Rare Earth Resource Utilization,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinsong Ren
- Laboratory of Chemical
Biology and State Key Laboratory of Rare Earth Resource Utilization,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaogang Qu
- Laboratory of Chemical
Biology and State Key Laboratory of Rare Earth Resource Utilization,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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24
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Selection and characterization of dimethylindole red DNA aptamers for the development of light-up fluorescent probes. Talanta 2017; 168:217-221. [PMID: 28391845 DOI: 10.1016/j.talanta.2017.03.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 03/16/2017] [Indexed: 01/12/2023]
Abstract
To develop novel label-free light-up probes with improved performance characteristics and low background, we selected DNA aptamers for dimethylindole red (DIR) by a modified affinity chromatography based SELEX method. DIR is an anionic propylsulfonate substituted red-emitting dye derivative of thiazole orange and exhibited weak fluorescence in fluid solution and in the presence of dsDNA. After 14 rounds of selection, a shortened 42-mer DNA aptamer with sub-micromolar dissociation constant (Kd=0.65±0.17μM) was selected. The fluorescent intensity of DIR was dramatically enhanced in the presence of the specific aptamer. The aptamer gave a 140-fold fluorescence enhancement in a saturated concentration. The DIR-aptamer pair could be potentially used as novel light-up fluorescent probe to construct sensors for various applications.
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25
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Huang Y, Ma Y, Li Y, Xiong M, Li X, Zhang L, Zhao S. Sensitive and label-free fluorescence detection of apurinic/apyrimidinic endonuclease 1 activity based on isothermal amplified-generation of G-quadruplex. NEW J CHEM 2017. [DOI: 10.1039/c6nj03477b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free and sensitive assay for apurinic/apyrimidinic endonuclease 1 was achieved based on isothermal amplification and G-quadruplex/ligand recognition.
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Affiliation(s)
- Yufeng Huang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
| | - Yefei Ma
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
| | - Yina Li
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
| | - Mei Xiong
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
| | - Xuejun Li
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources
- School of Chemistry and Pharmaceutical Sciences
- Guangxi Normal University
- Guilin 541004
- P. R. China
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26
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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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27
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Simple and convenient G-quadruplex-based fluorescent assay of biotin-streptavidin interaction via terminal protection of small molecule-linked DNA. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1980-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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28
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Sun P, Ran X, Liu C, Liu C, Pu F, Ren J, Qu X. DNA-fueled molecular machine for label-free and non-enzymatic ultrasensitive detection of telomerase activity. Analyst 2016; 141:4855-8. [PMID: 27405851 DOI: 10.1039/c6an00997b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Herein, a non-enzymatic and label-free strategy based on DNA-fueled molecular machine was developed for ultrasensitive detection of telomerase activity in cancer cell extracts even at the single-cell level.
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Affiliation(s)
- Panpan Sun
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiang Ran
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chaoying Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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29
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Lu L, Wang W, Yang C, Kang TS, Leung CH, Ma DL. Iridium(iii) complexes with 1,10-phenanthroline-based N^N ligands as highly selective luminescent G-quadruplex probes and application for switch-on ribonuclease H detection. J Mater Chem B 2016; 4:6791-6796. [DOI: 10.1039/c6tb02316a] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A study was performed to investigate the relationship between molecular structure and G4 sensing ability for a series of iridium(iii) complexes. The complex7was used to construct a G4-based assay for RNase H.
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Affiliation(s)
- Lihua Lu
- College of Chemistry and Pharmaceutical Sciences
- Qingdao Agricultural University
- Qingdao 266109
- China
- Department of Chemistry
| | - Wanhe Wang
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
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30
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Li K, Wang L, Xu X, Gao T, Yan P, Jiang W. Protein binding-protected DNA three-way junction-mediated rolling circle amplification for sensitive and specific detection of transcription factors. RSC Adv 2016. [DOI: 10.1039/c6ra12535b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A novel fluorescent strategy for transcription factors assay was developed based on protein binding-protected DNA three-way junction-mediated rolling circle amplification.
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Affiliation(s)
- Kan Li
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Lei Wang
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
- P. R. China
| | - Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Ting Gao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Ping Yan
- Jinan Maternity and Child Care Hospital
- 250001 Jinan
- P. R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
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31
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Wang J, Zhang Y, Wang H, Chen Y, Xu L, Gao T, Pei R. Selection and analysis of DNA aptamers to berberine to develop a label-free light-up fluorescent probe. NEW J CHEM 2016. [DOI: 10.1039/c6nj02290a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three DNA aptamers for berberine were successfully selected and the final shortened 21-mer aptamer showed higher fluorescence enhancement than G-quadruplexes.
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Affiliation(s)
- Jine Wang
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yajie Zhang
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Hongyan Wang
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yang Chen
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Tian Gao
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
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32
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Wang W, Kang TS, Chan PWH, Lu JJ, Chen XP, Leung CH, Ma DL. A label-free G-quadruplex-based mercury detection assay employing the exonuclease III-mediated cleavage of T-Hg 2+-T mismatched DNA. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2015; 16:065004. [PMID: 27877846 PMCID: PMC5069990 DOI: 10.1088/1468-6996/16/6/065004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 05/30/2023]
Abstract
We report herein the use of an exonuclease III and G-quadruplex probe to construct a G-quadruplex-based luminescence detection platform for Hg2+. Unlike common DNA-based Hg2+ detection methods, when using the dsDNA probe to monitor the hairpin formation, the intercalation of the dsDNA probe may be influenced by the distortion of dsDNA. This 'mix-and-detect' methodology utilized the G-quadruplex probe as the signal transducer and is simple, rapid, convenient to use and can detect down to 20 nM of Hg2+.
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Affiliation(s)
- Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Philip Wai Hong Chan
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xiu-Ping Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- Partner State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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33
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Guo Y, Yao W, Xie Y, Zhou X, Hu J, Pei R. Logic gates based on G-quadruplexes: principles and sensor applications. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1633-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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34
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Lin S, Gao W, Tian Z, Yang C, Lu L, Mergny JL, Leung CH, Ma DL. Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe. Chem Sci 2015; 6:4284-4290. [PMID: 29218197 PMCID: PMC5707507 DOI: 10.1039/c5sc01320h] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/17/2015] [Indexed: 12/22/2022] Open
Abstract
A series of luminescent iridium(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The iridium(iii) complex 9 [Ir(pbi)2(5,5-dmbpy)]PF6 (where pbi = 2-phenyl-1H-benzo[d]imidazole; 5,5-dmbpy = 5,5'-dimethyl-2,2'-bipyridine) exhibited high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a G-quadruplex-based assay for protein tyrosine kinase-7 (PTK7) in aqueous solution. PTK7 is an important biomarker for a range of leukemias and solid tumors. In the presence of PTK7, the specific binding of the sgc8 aptamer sequence triggers a structural transition and releases the G-quadruplex-forming sequence. The formation of the nascent G-quadruplex structure is then detected by the G-quadruplex-selective iridium(iii) complex with an enhanced luminescent response. Moreover, the application of the assay for detecting PTK7 in cellular debris and membrane protein extract was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for PTK7.
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Affiliation(s)
- Sheng Lin
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Wei Gao
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Zeru Tian
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Lihua Lu
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Jean-Louis Mergny
- University of Bordeaux , ARNA Laboratory , Bordeaux , France .
- INSERM , U869 , IECB , Pessac , France
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
- Partner State Key Laboratory of Environmental and Biological Analysis , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China
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35
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Recent Developments in G-Quadruplex Probes. ACTA ACUST UNITED AC 2015; 22:812-28. [DOI: 10.1016/j.chembiol.2015.06.016] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022]
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36
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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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37
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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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38
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Xu L, Shen X, Hong S, Wang J, Zhang Y, Wang H, Zhang J, Pei R. Turn-on and label-free fluorescence detection of lead ions based on target-induced G-quadruplex formation. Chem Commun (Camb) 2015; 51:8165-8. [DOI: 10.1039/c5cc01590a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Using a guanine-rich sequence (AGRO100) and N-methyl mesoporphyrin IX (NMM), a turn-on and label-free fluorescent Pb2+ sensor with high sensitivity and low background fluorescence was presented as a representative of five turn-on sensing systems.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Yuanyuan Zhang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Hongyan Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Jianye Zhang
- School of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
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39
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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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40
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He Y, Jiao B. Simple and convenient G-quadruplex-based fluorescence assay of micrococcal nuclease activity. RSC Adv 2015. [DOI: 10.1039/c5ra20773h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
An ultrasensitive and straightforward fluorescence sensing platform for MNase activity has been developed based on NMM/G-quadruplexes.
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Affiliation(s)
- Yue He
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing)
- Ministry of Agriculture
- Citrus Research Institute
- Southwest University
- Chongqing
| | - Bining Jiao
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing)
- Ministry of Agriculture
- Citrus Research Institute
- Southwest University
- Chongqing
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41
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Ma DL, Lin S, Lu L, Wang M, Hu C, Liu LJ, Ren K, Leung CH. G-quadruplex-based logic gates for HgII and AgI ions employing a luminescent iridium(iii) complex and extension of metal-mediated base pairs by polymerase. J Mater Chem B 2015; 3:4780-4785. [DOI: 10.1039/c5tb00718f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report herein the synthesis of a series of cyclometallated iridium(iii) complexes as luminescent G-quadruplex-selective probes to construct AND, OR and INHIBIT logic gates for the detection of HgII and AgI ions.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
- Partner State Key Laboratory of Environmental and Biological Analysis
| | - Sheng Lin
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Modi Wang
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Chong Hu
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Li-Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Kangning Ren
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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42
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Zhao D, Dong X, Jiang N, Zhang D, Liu C. Selective recognition of parallel and anti-parallel thrombin-binding aptamer G-quadruplexes by different fluorescent dyes. Nucleic Acids Res 2014; 42:11612-21. [PMID: 25245945 PMCID: PMC4191408 DOI: 10.1093/nar/gku833] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) have been found increasing potential in applications, such as molecular therapeutics, diagnostics and sensing. Both Thioflavin T (ThT) and N-Methyl mesoporphyrin IX (NMM) become fluorescent in the presence of most G4, but thrombin-binding aptamer (TBA) has been reported as the only exception of the known G4-forming oligonucleotides when ThT is used as a high-throughput assay to identify G4 formation. Here, we investigate the interactions between ThT/NMM and TBA through fluorescence spectroscopy, circular dichroism and molecular docking simulation experiments in the absence or presence of cations. The results display that a large ThT fluorescence enhancement can be observed only when ThT bind to the parallel TBA quadruplex, which is induced to form by ThT in the absence of cations. On the other hand, great promotion in NMM fluorescence can be obtained only in the presence of anti-parallel TBA quadruplex, which is induced to fold by K+ or thrombin. The highly selective recognition of TBA quadruplex with different topologies by the two probes may be useful to investigate the interactions between conformation-specific G4 and the associated proteins, and could also be applied in label-free fluorescent sensing of other biomolecules.
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Affiliation(s)
- Dan Zhao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xiongwei Dong
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Nan Jiang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Dan Zhang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Changlin Liu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan 430079, China
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43
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Guo Q, Chen Y, Song Z, Guo L, Fu F, Chen G. Label-free and enzyme-free sensitive fluorescent detection of human immunodeficiency virus deoxyribonucleic acid based on hybridization chain reaction. Anal Chim Acta 2014; 852:244-9. [PMID: 25441904 DOI: 10.1016/j.aca.2014.09.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 10/24/2022]
Abstract
A label-free and enzyme-free sensitive fluorescent detection of human immunodeficiency virus (HIV) deoxyribonucleic acid (DNA) based on isothermal hybridization chain reaction (HCR) was developed. A G-quadruplex sequence which was incorporated into one of the two hairpin probes was inactive in the absence of target DNA. However, at the presence of target DNA numerous G-quadruplexes along DNA nanowires were self-assembled through HCR. Using N-methyl mesoporphyrin IX (NMM) as the fluorophore, a "turn-on" fluorescent response would be achieved and detected as low as 0.5 nmol L(-1) of HIV DNA. This proposed method was applied to detect HIV DNA in biologic samples with satisfactory results.
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Affiliation(s)
- Qingquan Guo
- Ministry of Education Key Laboratory of Analysis and Detection for food safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Ying Chen
- Ministry of Education Key Laboratory of Analysis and Detection for food safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Zhiping Song
- Ministry of Education Key Laboratory of Analysis and Detection for food safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Liangqia Guo
- Ministry of Education Key Laboratory of Analysis and Detection for food safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China.
| | - Fengfu Fu
- Ministry of Education Key Laboratory of Analysis and Detection for food safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for food safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
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44
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Wang M, Leung KH, Lin S, Chan DSH, Leung CH, Ma DL. A G-quadruplex-based, label-free, switch-on luminescent detection assay for Ag+ions based on the exonuclease III-mediated digestion of C–Ag+–C DNA. J Mater Chem B 2014; 2:6467-6471. [DOI: 10.1039/c4tb01140f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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45
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Chen Z, Zhou L, Zhao A, Zhang Z, Wang Z, Lin Y, Ren J, Qu X. Coupling exonuclease III with DNA metallization for amplified detection of biothiols at picomolar concentration. Biosens Bioelectron 2014; 58:214-8. [DOI: 10.1016/j.bios.2014.02.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 02/14/2014] [Accepted: 02/18/2014] [Indexed: 11/29/2022]
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46
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A carbon nanotubes based fluorescent aptasensor for highly sensitive detection of adenosine deaminase activity and inhibitor screening in natural extracts. J Pharm Biomed Anal 2014; 95:164-8. [DOI: 10.1016/j.jpba.2014.02.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/24/2014] [Accepted: 02/27/2014] [Indexed: 12/31/2022]
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47
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Guo Y, Cheng J, Wang J, Zhou X, Hu J, Pei R. Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain. Chem Asian J 2014; 9:2397-401. [PMID: 24909844 DOI: 10.1002/asia.201402199] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 11/08/2022]
Abstract
A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction.
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Affiliation(s)
- Yahui Guo
- Suzhou Key Laboratory of Nanotheranostics, Division of Nanobiomedicine, Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 (P.R. China); Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry & Molecular Sciences, Wuhan University, Wuhan, 430072 (P.R. China)
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48
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A highly sensitive label-free sensor for Mercury ion (Hg²⁺) by inhibiting thioflavin T as DNA G-quadruplexes fluorescent inducer. Talanta 2014; 122:85-90. [PMID: 24720966 DOI: 10.1016/j.talanta.2014.01.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/21/2014] [Accepted: 01/23/2014] [Indexed: 11/20/2022]
Abstract
DNA sequences with guanine repeats can be induced to form G-quartets that adopt G-quadruplex structures in the presence of thioflavin T (ThT). ThT plays a dual role of inducing DNA sequences to fold into quadruplex structures and of sensing the change by its remarkable fluorescence enhancement. ThT binding to the DNA sequences with guanine repeats showed highly specific fluorescence enhancement compared with single/double-stranded DNA. In this work, we have utilized the conformational switch from G-quadruplex complex induced by fluorogenic dye ThT to Hg(2+) mediated T-Hg-T double-stranded DNA formation, thereby pioneering a facile approach to detect Hg(2+) with fluorescence spectrometry. Through this approach, Hg(2+) in aqueous solutions can be detected at 5 nM with fluorescence spectrometry in a facile way, with high selectivity against other metal ions. These results indicate the introduced label-free method for fluorescence spectrometric Hg(2+) detection is simple, quantitative, sensitive, and highly selective.
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49
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Lin S, He B, Shiu-Hin Chan D, Hong Chan PW, Leung CH, Ma DL. A G-quadruplex-based platform for the detection of Hg2+ ions using a luminescent iridium(iii) complex. RSC Adv 2014. [DOI: 10.1039/c4ra11240g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report herein the synthesis of a series of cyclometalated iridium(iii) complexes as luminescent G-quadruplex-selective probes, which were used to construct an oligonucleotide-based platform for the dual detection and removal of Hg2+ ions.
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Affiliation(s)
- Sheng Lin
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong, China
| | - Bingyong He
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong, China
| | | | - Philip Wai Hong Chan
- School of Chemistry
- Monash University
- , Australia
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao, China
| | - Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong, China
- Partner State Key Laboratory of Environmental and Biological Analysis
- Hong Kong Baptist University
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50
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Li H, Ren J, Liu Y, Wang E. Application of DNA machine in amplified DNA detection. Chem Commun (Camb) 2014; 50:704-6. [DOI: 10.1039/c3cc47147k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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