1
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Na H, Koo BI, Park JC, Lim J, Kim Y, Chung HJ, Nam YS. Live-Cell Imaging of MicroRNA Expression via Photoinduced Electron Transfer Controlled by Catalytic Hairpin Assembly. Adv Healthc Mater 2024:e2401483. [PMID: 38889395 DOI: 10.1002/adhm.202401483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 06/20/2024]
Abstract
MicroRNAs (miRNAs) serve as emerging biomarkers for a range of diseases, and their quantitative analysis draws increasing attention. Yet, current invasive methods limit continuous tracking within living cells. To overcome this, a nonenzymatic DNA-based nanoprobe is developed for dynamic, noninvasive miRNA tracking via live-cell imaging. This probe features a unique hairpin DNA structure with five guanines that act as internal quenchers, suppressing fluorescence from an attached fluorophore via photoinduced electron transfer. Target miRNA initiates toehold-mediated strand displacement, restoring, and amplifying the fluorescence signal. Additionally, by introducing a single mismatch to the hairpin DNA, the nanoprobe's sensitivity is significantly enhanced, lowering the detection limit to about 60 pM without compromising specificity. To optimize intracellular delivery for prolonged monitoring, the nanoprobe is encapsulated within multilamellar lipid nanovesicles, fluorescently labeled for dual-wavelength ratiometric analysis. The proposed nanoprobe demonstrates a significant advance in live-cell miRNA detection, promising enhanced in situ analysis for a better understanding of miRNAs' pathophysiological function.
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Affiliation(s)
- Hyebin Na
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Bon Il Koo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jae Chul Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jiwoo Lim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoon Sung Nam
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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2
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Lim RC, Gary RK. Kinetic analysis of T4 polynucleotide kinase via isothermal titration calorimetry. Arch Biochem Biophys 2024; 756:109995. [PMID: 38621448 DOI: 10.1016/j.abb.2024.109995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
T4 polynucleotide kinase (T4 PNK) phosphorylates the 5'-terminus of DNA and RNA substrates. It is widely used in molecular biology. Single nucleotides can serve as substrates if a 3'-phosphate group is present. In this study, the T4 PNK-catalyzed conversion of adenosine 3'-monophosphate (3'-AMP) to adenosine-3',5'-bisphosphate was characterized using isothermal titration calorimetry (ITC). Although ITC is typically used to study ligand binding, in this case the instrument was used to evaluate enzyme kinetics by monitoring the heat production due to reaction enthalpy. The reaction was initiated with a single injection of 3'-AMP substrate into the sample cell containing T4 PNK and ATP at pH 7.6 and 30 °C, and Michaelis-Menten analysis was performed on the reaction rates derived from the plot of differential power versus time. The Michaelis-Menten constant, KM, was 13 μM, and the turnover number, kcat, was 8 s-1. The effect of inhibitors was investigated using pyrophosphate (PPi). PPi caused a dose-dependent decrease in the apparent kcat and increase in the apparent KM under the conditions tested. Additionally, the intrinsic reaction enthalpy and the activation energy of the T4 PNK-catalyzed phosphorylation of 3'-AMP were determined to be -25 kJ/mol and 43 kJ/mol, respectively. ITC is seldom used as a tool to study enzyme kinetics, particularly for technically-challenging enzymes such as kinases. This study demonstrates that quantitative analysis of kinase activity can be amenable to the ITC single injection approach.
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Affiliation(s)
- Rebecca C Lim
- Department of Chemistry & Biochemistry, University of Nevada, Las Vegas, USA
| | - Ronald K Gary
- Department of Chemistry & Biochemistry, University of Nevada, Las Vegas, USA.
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3
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Si J, Zhou W, Fang Y, Zhou D, Gao Y, Yao Q, Shen X, Zhu C. Label-Free Detection of T4 Polynucleotide Kinase Activity and Inhibition via Malachite Green Aptamer Generated from Ligation-Triggered Transcription. BIOSENSORS 2023; 13:bios13040449. [PMID: 37185524 PMCID: PMC10135927 DOI: 10.3390/bios13040449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Polynucleotide kinase (PNK) is a key enzyme that is necessary for ligation-based DNA repair. The activity assay and inhibitor screening for PNK may contribute to the prediction and improvement of tumor treatment sensitivity, respectively. Herein, we developed a simple, low-background, and label-free method for both T4 PNK activity detection and inhibitor screening by combining a designed ligation-triggered T7 transcriptional amplification system and a crafty light-up malachite green aptamer. Moreover, this method successfully detected PNK activity in the complex biological matrix with satisfactory outcomes, indicating its great potential in clinical practice.
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Affiliation(s)
- Jingyi Si
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Zhou
- Department of School and Nutrition, Shanghai Yangpu District Center for Disease Control and Prevention, Shanghai 200090, China
| | - Ying Fang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Da Zhou
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yifan Gao
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qunyan Yao
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Changfeng Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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4
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Liu XW, Liu WJ, Meng Y, Hu J, Zhang CY. Development of a tandem signal amplification strategy for label-free sensing polynucleotide kinase activity in cancer cells. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Liu J, Liu Y, Zhang L, Fu S, Su X. Ultra-specific fluorescence detection of DNA modifying enzymes by dissipation system. Biosens Bioelectron 2022; 215:114561. [PMID: 35841766 DOI: 10.1016/j.bios.2022.114561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022]
Abstract
Abnormal expression of DNA modifying enzymes (DMEs) is linked to a variety of diseases including cancers. It is desirable to develop accurate methods for DME detection. However, the substrate-based probe for target DMEs is disturbed by various non-target DMEs that have similar activity resulting in a loss of specificity. Here we utilized dissipative DNA networks to develop an ultra-specific fluorescence assay for DME, absolutely distinguishing between target and non-target enzymes. Unlike the conventional sensors in which the discrimination of target and non-target relies on signal intensity, in our system, target DMEs exhibit featured fluorescence oscillatory signals, while non-target DMEs show irreversible 'one-way' fluorescence increase. These dissipation-enabled probes (DEPs) exhibit excellent generality for various types of DMEs including DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1), polynucleotide kinase (T4 PNK), and methyltransferase (Dam). DEPs provide a novel quantification mode based on area under curve which is more robust than those intensity-based quantifications. The detection limits of APE1, T4 PNK, and Dam reach 0.025 U/mL, 0.44 U/mL, and 0.113 U/mL, respectively. DEPs can accurately identify their corresponding DMEs with excellent specificity in cell extracts. Fluorescence sensors based on DEPs herein represent a conceptually new class of methods for enzyme detection, which can be easily adapted to other sensing platforms such as electrochemical sensors.
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Affiliation(s)
- Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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6
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Xu L, Zhao W, Pu J, Wang S, Liu S, Li H, Yu R. A Pax-5a gene analysis approach enabled by selective digestion with lambda exonuclease. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2415-2422. [PMID: 35670541 DOI: 10.1039/d2ay00469k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Owing to the rapid increase in acute leukemia patients, the detection of Pax-5a, which is a tumor marker, is very important for the early diagnosis of patients. Therefore, by combining the selective digestion function of lambda exonuclease and the hybridization chain reaction (HCR) enzyme-free amplification system, we design a biosensor to detect the Pax-5a gene with high sensitivity. Lambda exonuclease can cleave the blunt end formed by the hairpin probe and the Pax-5a gene, which exposes the nucleic acid sequence that can initiate the HCR. When the HCR is triggered, the fluorophore and quencher on H1 and H2 move away from each other, so that the fluorescence signal of the quenched fluorophore can be recovered. Under optimal experimental conditions, a good linear relationship was established between the fluorescence intensity and the logarithm of the target concentration, and the limit of detection (LOD) of Pax-5a was calculated to be 7.6 pM. In addition, the biosensor can not only discriminate the base mismatch sequences of the Pax-5a gene, but also be suitable for target detection in complex human serum samples. Therefore, this biosensor, with the advantages of simple operation, high sensitivity, and good selectivity, has a good application prospect and guiding role in the diagnosis of acute B lymphocytic leukemia and the design of biosensors.
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Affiliation(s)
- LianLian Xu
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Weihua Zhao
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Jiamei Pu
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Suqin Wang
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Shiwen Liu
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, P. R. China
| | - Hongbo Li
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou 215123, P. R. China
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
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7
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Zhang T, Shen Y, Ge J, Wang W, Qu L, Li Z. A highly sensitive fluorescence method for the detection of T4 polynucleotide kinase phosphatase based on polydopamine nanotubes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120594. [PMID: 34776378 DOI: 10.1016/j.saa.2021.120594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
T4 polynucleotide kinase phosphatase (T4 PNKP) plays a critical role in various cellular events, such as DNA damage repair, replication, and recombination. Here, we have described a novel biosensor to detect the activity of T4 PNKP based on polydopamine nanotubes (PDANTs) mediated fluorescence resonance energy transfer (FRET). A FAM-labelled (6-carboxyl-fluorescein) hairpin DNA probe with 3'-phosphoryl terminal was designed as the substrate for T4 PNKP. With the addition of PDANTs, the fluorescence of FAM-labelled hairpin DNA probe could be quenched because of the high adsorption of hairpin DNA on PDANTs. When T4 PNKP dephosphorylated the DNA probe, a double-stranded DNA (dsDNA) product was obtained by Klenow fragment polymerase (KF polymerase) on its 3'-hydroxyl terminal, which could retain most of the fluorescence due to the week adsorption of dsDNA on PDANTs. The developed method demonstrates the sensitivity for T4 PNKP assay in the range from 0.05 to 1.5 U mL-1 with the detection limit of 0.005 U mL-1, which endows the proposed strategy with high enough sensitivity for practical detection in cell lysates. With the advantages mentioned above, this novel sensitive strategy has the potential in the study of DNA damage repair mechanisms.
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Affiliation(s)
- Tuo Zhang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yanmei Shen
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Jia Ge
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China.
| | - Weixia Wang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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8
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Jiang X, Shen X, Talap J, Yang D, Zeng S, Liu H, Cai S. Phosphorothioated and phosphate-terminal dumbbell (PP-TD) probe-based rapid detection of polynucleotide kinase activity. Analyst 2022; 147:4986-4990. [DOI: 10.1039/d2an01431a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A primer-free, sensitive assay has been developed to detect polynucleotide kinase (PNK) activity. This proposed method provides a promising platform for PNK activity monitoring and inhibition screening for drug discovery and clinical treatment.
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Affiliation(s)
- Xianfeng Jiang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, China
| | - Xudan Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
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9
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Li Y, Liu Q, Cui L, Liu W, Qiu JG, Zhang CY. Zirconium ion-mediated assembly of a single quantum dot-based nanosensor for kinase assay. Chem Commun (Camb) 2021; 57:6376-6379. [PMID: 34081069 DOI: 10.1039/d1cc02035h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate the zirconium ion-mediated assembly of a single quantum dot (QD)-based nanosensor for accurate detection of protein kinases (PKA) and polynucleotide kinases (PNK). This nanosensor is very sensitive with a detection limit of 8.82 × 10-4 U mL-1 for PKA and 1.40 × 10-5 U mL-1 for PNK. Moreover, it can be used to analyze the enzyme kinetic parameters and screen the inhibitors of PKA and PNK, with potential applications in drug discovery and clinical diagnosis.
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Affiliation(s)
- Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Qian Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Wenjing Liu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Jian-Ge Qiu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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10
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Hu C, Jiang K, Shao Z, Shi M, Meng HM. A DNAzyme-based label-free fluorescent probe for guanosine-5'-triphosphate detection. Analyst 2021; 145:6948-6954. [PMID: 32852000 DOI: 10.1039/d0an01334j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Guanosine-5'-triphosphate (GTP) plays a key role in many important biological processes of cells. It is not only a primer for DNA replication and one of the four essential nucleoside triphosphates for mRNA synthesis, but also an energy source for translation and other important cellular processes. It can be converted to adenine nucleoside triphosphate (ATP), and the intracellular GTP level is closely related to the specific pathological state, so it is crucial to establish a simple and accurate method for the detection of GTP. Deoxyribozymes have unique catalytic and structural properties. One of the deoxyribozymes which is named DK2 with self-phosphorylation ability can transfer a phosphate from GTP to the 5' end in the presence of manganese(ii), while lambda exonuclease (λexo) catalyzes the gradual hydrolysis of double-stranded DNA molecules phosphorylated at the 5'-end from 5' to 3', but cannot cleave the 5'-OH end. The fluorescent dye SYBR Green I (SG I) can bind to dsDNA and produce significant fluorescence, but it can only give out weak fluorescence when it is mixed with a single strand. Here, we present a novel unlabeled fluorescence assay for GTP based on the self-phosphorylation of deoxyribozyme DK2 and the specific hydrolysis of λexo. Owing to the advantages of simple operation, high sensitivity, good specificity, low cost and without fluorophore (quenching group) labeling, this method has great potential in biological applications.
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Affiliation(s)
- Chengzhen Hu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China.
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11
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Cao X, Sun Y, Lu P, Zhao M. Fluorescence imaging of intracellular nucleases-A review. Anal Chim Acta 2020; 1137:225-237. [PMID: 33153605 DOI: 10.1016/j.aca.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Nucleases play crucial roles in maintaining genomic integrity. Visualization of intracellular distribution and translocation of nucleases are of great importance for understanding the in-vivo physiological functions of these enzymes and their roles in DNA repair and other cellular signaling pathways. Here we review the recently developed approaches for fluorescence imaging of nucleases in various eukaryotic cells. We mainly focused on the immunofluorescence techniques, the genetically encoded fluorescent probes and the chemically synthesized fluorescent DNA-substrate probes that enabled in-situ visualization of the subcellular localization of nucleases and their interactions with other protein/DNA molecules within cells. The targeted nucleases included important endonucleases, 3' exonucleases and 5' exonucleases that were involved in the DNA damage repair pathways and the intracellular DNA degradation. The advantages and limitations of the available tools were summarized and discussed.
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Affiliation(s)
- Xiangjian Cao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ying Sun
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peng Lu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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12
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Oladepo SA, Yusuf BO. Detection of Several Homologous MicroRNAs by a Single Smart Probe System Consisting of Linear Nucleic Acid Blockers. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24203691. [PMID: 31615053 PMCID: PMC6832958 DOI: 10.3390/molecules24203691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/01/2019] [Accepted: 10/05/2019] [Indexed: 11/13/2022]
Abstract
We report a universal smart probe (SP) that is capable of detecting several homologous let-7 microRNAs (miRNAs). While the SP is complementary to let-7a, and therefore, strongly binds to this target, due to sequence homology, the SP also has equal propensity to non-specifically hybridize with let-7b and let-7c, which are homologous to let-7a. The fluorescence signal of the SP was switched off in the absence of any homologous member target, but the signal was switched on when any of the three homologous members was present. With the assistance of nucleic acid blockers (NABs), this SP system can discriminate between homologous miRNAs. We show that the SP can discriminate between let-7a and the other two sequences by using linear NABs (LNABs) to block non-specific interactions between the SP and these sequences. We also found that LNABs used do not cross-react with the let-7a target due to the low LNABs:SP molar ratio of 6:1 used. Overall, this SP represents a universal probe for the recognition of a homologous miRNA family. The assay is sensitive, providing a detection limit of 6 fmol. The approach is simple, fast, usable at room temperature, and represents a general platform for the in vitro detection of homologous microRNAs by a single fluorescent hairpin probe.
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Affiliation(s)
- Sulayman A Oladepo
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
| | - Basiru O Yusuf
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
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13
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Wang M, Kong D, Su D, Liu Y, Su X. Ratio fluorescence analysis of T4 polynucleotide kinase activity based on the formation of a graphene quantum dot-copper nanocluster nanohybrid. NANOSCALE 2019; 11:13903-13908. [PMID: 31304938 DOI: 10.1039/c9nr02901j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, a ratio fluorescence method was developed for T4 polynucleotide kinase (PNK) activity analysis based on the formation of a dual-emitting graphene quantum dot-copper nanocluster (GQD-CuNC) nanohybrid. An amino capped single-strand DNA (ssDNA) was firstly used to modify GQDs (GQD-ssDNA) and then hybridize with its complementary DNA strand to form double-stranded DNA functionalized GQDs (GQD-dsDNA). The dsDNA of GQD-dsDNA can act as an effective template for the preparation of CuNCs with fluorescence emission at 594 nm. When the dsDNA of GQD-dsDNA was phosphorylated through T4 PNK and subsequently degraded via λ exonuclease (λ exo) to produce mononucleotides and GQD-ssDNA, the formation of fluorescence CuNCs in GQD-CuNCs was blocked due to the lack of an effective dsDNA substrate, during which the fluorescence of GQDs at 446 nm in the nanohybrid was mostly not influenced. Thus, with the CuNCs serving as the reporter and GQDs as the reference signal, T4 PNK activity can be monitored through the change in the fluorescence intensity ratio (F594/F446) in the range of 0.01-10 U mL-1 with a detection limit (LOD) of 0.0037 U mL-1. Furthermore, the practicality of this T4 PNK activity analysis strategy in a complex sample was tested in cell lysates.
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Affiliation(s)
- Mengke Wang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Deshuai Kong
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, PR China
| | - Dandan Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Yang Liu
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Xingguang Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
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14
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Wu T, Yang Y, Chen W, Wang J, Yang Z, Wang S, Xiao X, Li M, Zhao M. Noncanonical substrate preference of lambda exonuclease for 5'-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction. Nucleic Acids Res 2019; 46:3119-3129. [PMID: 29490081 PMCID: PMC5888420 DOI: 10.1093/nar/gky154] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/19/2018] [Indexed: 01/01/2023] Open
Abstract
Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Currently, it is also a widely used enzymatic tool in genetic engineering, DNA-binding protein mapping, nanopore sequencing and biosensing. Herein, we disclose two noncanonical properties of this enzyme and suggest a previously undescribed hydrophobic interaction model between λ exo and DNA substrates. We demonstrate that the length of the free portion of the substrate strand in the dsDNA plays an essential role in the initiation of digestion reactions by λ exo. A dsDNA with a 5' non-phosphorylated, two-nucleotide-protruding end can be digested by λ exo with very high efficiency. Moreover, we show that when a conjugated structure is covalently attached to an internal base of the dsDNA, the presence of a single mismatched base pair at the 5' side of the modified base may significantly accelerate the process of digestion by λ exo. A detailed comparison study revealed additional π-π stacking interactions between the attached label and the amino acid residues of the enzyme. These new findings not only broaden our knowledge of the enzyme but will also be very useful for research on DNA repair and in vitro processing of nucleic acids.
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Affiliation(s)
- Tongbo Wu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yufei Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing NMR Center, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shenlin Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing NMR Center, Peking University, Beijing 100871, China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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15
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Zhang Y, Zhao J, Chen S, Li S, Zhao S. A novel microchip electrophoresis laser induced fluorescence detection method for the assay of T4 polynucleotide kinase activity and inhibitors. Talanta 2019; 202:317-322. [PMID: 31171188 DOI: 10.1016/j.talanta.2019.05.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/01/2019] [Accepted: 05/04/2019] [Indexed: 12/19/2022]
Abstract
T4 polynucleotide kinase (T4 PNK) may catalyze the phosphorylation of 5'-hydroxyl termini in nucleic acids, which play a crucial role in DNA recombination, replication and damage repair. Here, a microchip electrophoresis laser induced fluorescence (MCE-LIF) method based on biochemical reaction was developed for the detection of T4 PNK activity and inhibitors. In this method, the single strand DNA (ssDNA) was hybridized with the 5-carboxyfluorescein (FAM) labeled single strand DNA (ssDNA-FAM) to form FAM labeled double-stranded DNA (dsDNA-FAM). In the presence of T4 PNK and adenosine triphosphate (ATP), T4 PNK catalyzes the transfer of γ-phosphate residues from ATP to the 5-hydroxyl terminal of dsDNA-FAM. The phosphorylated dsDNA-FAM can be gradually hydrolyzed by λexo to produce a FAM labeled single nucleotide fragment. Then the FAM labeled single nucleotide fragment and the unhydrolyzed dsDNA-FAM were separated by MCE, and two electrophoresis peaks appeared in the electrophoretogram. The detection of T4 PNK activity and inhibitors was realized by measuring the peak height of the FAM labeled single nucleotide fragment in electrophoretogram. This assay is very sensitive with a limit of detection of 0.002 U/mL, and it can be further used to screen the T4 PNK inhibitors.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004, China
| | - Jingjin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004, China.
| | - Shenyu Chen
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004, China
| | - Shuting Li
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, 541004, China.
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16
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Li N, Du M, Tian S, Ji X, He Z. The behavior of a bipedal DNA walker moving on the surface of magnet microparticles and its application in DNA detection. Anal Bioanal Chem 2019; 411:4055-4061. [PMID: 30693369 DOI: 10.1007/s00216-019-01604-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/16/2018] [Accepted: 01/11/2019] [Indexed: 12/26/2022]
Abstract
In this work, a three-dimensional DNA machine based on the isothermal strand-displacement polymerase reaction (ISDPR) has been constructed. The walking behavior of a DNA walker on the obstructive surface of magnetic beads has also been studied by adding different nucleic acid blocks. The "leg" of the DNA walker could hybridize with a hairpin structure DNA named H1 and lead to the opening of it. And the newly exposed stem would interact with a primer. A strand exchange has happened with the assistance of polymerase and dNTPs, so that the "leg" has been displaced and the DNA walker could be pushed to move on the surface. But the nucleic acid blocks could increase steric hindrance and obstruct this process, which is similar to the behavior of human beings walking on craggy paths. Through changing these blocks, such as the structure, the amount, and the length of blocks, the movement of the DNA walker has been controlled. What's more, the results of its application for DNA detection are satisfactory. The limit of detection is 21.6 pM. Also, this method has been successfully applied in complex biological samples. Graphical abstract ᅟ.
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Affiliation(s)
- Ningxing Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Mingyuan Du
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Songbai Tian
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
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17
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Zhou H, Tong C, Zou W, Yang Y, Liu Y, Li B, Qin Y, Dang W, Liu B, Wang W. A novel fluorescence method for activity assay and drug screening of T4 PNK by coupling rGO with ligase reaction. Analyst 2019; 144:1187-1196. [DOI: 10.1039/c8an02147c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
T4 polynucleotide kinase (PNK) is the primary member of the 5′-kinase family that can transfer the γ-phosphate residue of ATP to the 5′-hydroxyl group of oligonucleotides.
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Affiliation(s)
| | - Chunyi Tong
- College of Biology
- Hunan University
- Changsha
- China
| | - Wei Zou
- NHC key laboratory of birth defects research
- prevention and treatment
- Hunan Provincial Maternal and Child Health Care Hospital
- Changsha 410008
- PR China
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Yongbei Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Yan Qin
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Wenya Dang
- College of Biology
- Hunan University
- Changsha
- China
| | - Bin Liu
- College of Biology
- Hunan University
- Changsha
- China
- TCM and Ethnomedicine Innovation & Development International Laboratory
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
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18
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Zhang YP, Cui YX, Li XY, Du YC, Tang AN, Kong DM. A modified exponential amplification reaction (EXPAR) with an improved signal-to-noise ratio for ultrasensitive detection of polynucleotide kinase. Chem Commun (Camb) 2019; 55:7611-7614. [DOI: 10.1039/c9cc03568k] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We reported a modified exponential amplification reaction strategy and applied it to design an ultrasensitive biosensor for the detection of endogenous polynucleotide kinase activity at single-cell level.
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Affiliation(s)
- Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
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19
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Abstract
DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.
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Affiliation(s)
- David L. Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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20
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Cen Y, Deng WJ, Yu RQ, Chu X. Sensitive fluorescence sensing of T4 polynucleotide kinase activity and inhibition based on DNA/polydopamine nanospheres platform. Talanta 2018; 180:271-276. [DOI: 10.1016/j.talanta.2017.12.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 12/14/2022]
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21
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Li L, Zhao Y, Yu R, Chen T, Chu X. Novel Sensitive Fluorometric Determination of Exonuclease I Using Polydopamine Nanospheres. ANAL LETT 2018. [DOI: 10.1080/00032719.2017.1368530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Li Li
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Yanyan Zhao
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Ruqin Yu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Tingting Chen
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Xia Chu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
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22
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Oladepo SA. Design and Characterization of a Singly Labeled Fluorescent Smart Probe for In Vitro Detection of miR-21. APPLIED SPECTROSCOPY 2018; 72:79-88. [PMID: 28946749 DOI: 10.1177/0003702817736527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A sensitive hairpin smart probe (SP) has been developed and tested for its sequence-specificity and sensitivity for detecting microRNAs (miRNAs). The loop sequence of this SP is perfectly complementary to microRNA-21 (miR-21) sequence. This miRNA regulates certain biological processes and has been implicated in certain forms of cancer. The stem of the new SP consists of a fluorophore on one end and multiple guanine bases on the opposing end are used as quenchers. The fluorescence of the SP is significantly quenched by the guanine bases at room temperature and in the absence of the miR-21 target. The presence of miR-21 switches on the fluorescence due to spontaneous hybridization of the SP with this target, which also forces the stem hybrid of the SP apart. This new SP successfully discriminated between the perfect miR-21 target and two closely similar single-base mismatch sequences. When the SP was incubated with the miR-21 at 37 ℃, the hybridization kinetics increased seven times, compared to room temperature hybridization. Overall, this new SP shows good detection sensitivity and gives a limit of detection and limit of quantitation of 14.0 nM and 46.7 nM, respectively. This detection platform represents a simple, fast, mix-and-read homogeneous assay for sequence-specific detection of miR-21, and it can be adapted for other related diagnostic applications.
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Affiliation(s)
- Sulayman A Oladepo
- 108765 Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
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23
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Liu M, Ma F, Zhang Q, Zhang CY. Label-free and ultrasensitive detection of polynucleotide kinase activity at the single-cell level. Chem Commun (Camb) 2018; 54:1583-1586. [DOI: 10.1039/c7cc09573b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We develop a label-free fluorescence method for the polynucleotide kinase assay at the single-cell level based on phosphorylation-triggered isothermal exponential amplification.
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Affiliation(s)
- Meng Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | | | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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24
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Gao M, Guo J, Song Y, Zhu Z, Yang CJ. Detection of T4 Polynucleotide Kinase via Allosteric Aptamer Probe Platform. ACS APPLIED MATERIALS & INTERFACES 2017; 9:38356-38363. [PMID: 29027787 DOI: 10.1021/acsami.7b14185] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As a vital enzyme in DNA phosphorylation and restoration, T4 polynucleotide kinase (T4 PNK) has aroused great interest in recent years. Therefore, numerous strategies have been established for highly sensitive detection of T4 PNK based on diverse signal amplification techniques. However, they often need sophisticated design, a variety of auxiliary reagents and enzymes, or cumbersome manipulations. We have designed a new kind of allosteric aptamer probe (AAP) consisting of streptavidin (SA) aptamer and the complementary DNA (cDNA) for simple detection of T4 PNK without signal amplification and with minimized interference in complex biological samples. When the 5'-terminus of the cDNA is phosphorylated by T4 PNK, the cDNA is degraded by lambda exonuclease to release the fluorescein amidite (FAM)-labeled SA aptamer, which subsequently binds to streptavidin beads. The enhancement of the fluorescence signal on SA beads can be detected precisely and easily by a microscope or flow cytometer. Our method performs well in complex biological samples as a result of the enrichment of the signaling molecules on beads, as well as simple manipulations to discard the background interference and nonbinding molecules. Without signal amplification techniques, our AAP method not only avoids complicated manipulations but also decreases the time required. With the advantages of ease of operation, reliability, and robustness for T4 PNK detection in buffer as well as real biological samples, the AAP has great potential for clinical diagnostics, inhibitor screening, and drug discovery.
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Affiliation(s)
- Mingxuan Gao
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Jingjing Guo
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Yanling Song
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
- The Key Lab of Analysis and Detection Technology for Food Safety of MOE, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Chaoyong James Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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25
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Dumbbell DNA-templated CuNPs as a nano-fluorescent probe for detection of enzymes involved in ligase-mediated DNA repair. Biosens Bioelectron 2017; 94:456-463. [DOI: 10.1016/j.bios.2017.03.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 11/23/2022]
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26
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Wang LJ, Zhang Q, Tang B, Zhang CY. Single-Molecule Detection of Polynucleotide Kinase Based on Phosphorylation-Directed Recovery of Fluorescence Quenched by Au Nanoparticles. Anal Chem 2017; 89:7255-7261. [PMID: 28585816 DOI: 10.1021/acs.analchem.7b01783] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
5'-Polynucleotide kinase such as T4 polynucleotide kinase (T4 PNK) may catalyze the phosphorylation of 5'-hydroxyl termini in nucleic acids, playing a crucial role in DNA replication, DNA recombination, and DNA damage repair. Here, we demonstrate for the first time single-molecule detection of PNK based on phosphorylation-directed recovery of fluorescence quenched by Au nanoparticle (AuNP) in combination with lambda exonuclease-mediated cleavage reaction. In the presence of PNK, the γ-phosphate group from adenosine triphosphate (ATP) is transferred to 5'-hydroxyl terminus, resulting in 5'-phosphorylation of the hairpin probe. The phosphorylated hairpin probes may function as the substrates of lambda exonuclease and enable the removal of 5' mononucleotides from the stem, leading to the unfolding of hairpin structure and the formation of binding probes. The resultant binding probes may specifically hybridize with the AuNP-modified capture probes, forming double-strand DNA (dsDNA) duplexes with 5'-phosphate groups as the substrates of lambda exonuclease and subsequently leading to the cleavage of capture probes and the liberation of Cy5 molecules and the binding probes. The released binding probes may further hybridize with new capture probes, inducing cycles of digestion-release-hybridization and consequently the release of numerous Cy5 molecules. Through simply monitoring Cy5 molecules with total internal reflection fluorescence (TIRF)-based imaging, PNK activity can be quantitatively measured. This assay is very sensitive with a limit of detection of 9.77 × 10-8 U/μL, and it may be further used to screen the PNK inhibitors and measure PNK in cancer cell extracts.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University , Jinan 250014, China
| | - Qianyi Zhang
- Nantou High School Shenzhen , Shenzhen, 518052, China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University , Jinan 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University , Jinan 250014, China
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27
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Ma DL, Dong ZZ, Vellaisamy K, Cheung KM, Yang G, Leung CH. Luminescent Strategies for Label-Free G-Quadruplex-Based Enzyme Activity Sensing. CHEM REC 2017; 17:1135-1145. [PMID: 28467681 DOI: 10.1002/tcr.201700014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 12/30/2022]
Abstract
By catalyzing highly specific and tightly controlled chemical reactions, enzymes are essential to maintaining normal cellular physiology. However, aberrant enzymatic activity can be linked to the pathogenesis of various diseases. Therefore, the unusual activity of particular enzymes can represent testable biomarkers for the diagnosis or screening of certain diseases. In recent years, G-quadruplex-based platforms have attracted wide attention for the monitoring of enzymatic activities. In this Personal Account, we discuss our group's works on the development of G-quadruplex-based sensing system for enzyme activities by using mainly iridium(III) complexes as luminescent label-free probes. These studies showcase the versatility of the G-quadruplex for developing assays for a variety of different enzymes.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Zhen-Zhen Dong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | | | - Ka-Man Cheung
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Guanjun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
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28
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Li X, Xu X, Song J, Xue Q, Li C, Jiang W. Sensitive detection of T4 polynucleotide kinase activity based on multifunctional magnetic probes and polymerization nicking reactions mediated hyperbranched rolling circle amplification. Biosens Bioelectron 2017; 91:631-636. [DOI: 10.1016/j.bios.2017.01.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/22/2016] [Accepted: 01/11/2017] [Indexed: 11/26/2022]
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29
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Quencher-Free Fluorescence Method for the Detection of Mercury(II) Based on Polymerase-Aided Photoinduced Electron Transfer Strategy. SENSORS 2016; 16:s16111945. [PMID: 27869723 PMCID: PMC5134604 DOI: 10.3390/s16111945] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/10/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022]
Abstract
A new quencher-free Hg2+ ion assay method was developed based on polymerase-assisted photoinduced electron transfer (PIET). In this approach, a probe is designed with a mercury ion recognition sequence (MRS) that is composed of two T-rich functional areas separated by a spacer of random bases at the 3′-end, and a sequence of stacked cytosines at the 5′-end, to which a fluorescein (FAM) is attached. Upon addition of Hg2+ ions into this sensing system, the MRS folds into a hairpin structure at the 3′-end with Hg2+-mediated base pairs. In the presence of DNA polymerase, it will catalyze the extension reaction, resulting in the formation of stacked guanines, which will instantly quench the fluorescence of FAM through PIET. Under optimal conditions, the limit of detection for Hg2+ ions was estimated to be 5 nM which is higher than the US Environmental Protection Agency (EPA) standard limit. In addition, no labeling with a quencher was requiring, and the present method is fairly simple, fast and low cost. It is expected that this cost-effective fluorescence method might hold considerable potential in the detection of Hg2+ ions in real biological and environmental samples.
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Zhang H, Zhao Z, Lei Z, Wang Z. Sensitive Detection of Polynucleotide Kinase Activity by Paper-Based Fluorescence Assay with λ Exonuclease Assistance. Anal Chem 2016; 88:11358-11363. [DOI: 10.1021/acs.analchem.6b03567] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hua Zhang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
| | - Zhen Zhao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
- University
of
Chinese Academy of Sciences, No. 19A
Yuquan Road, Beijing, 100049, People’s Republic of China
| | - Zhen Lei
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
- University
of
Chinese Academy of Sciences, No. 19A
Yuquan Road, Beijing, 100049, People’s Republic of China
| | - Zhenxin Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
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Ma DL, Wang M, Liu C, Miao X, Kang TS, Leung CH. Metal complexes for the detection of disease-related protein biomarkers. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Xu J, Gao Y, Li B, Jin Y. Cyclic up-regulation fluorescence of pyrene excimer for studying polynucleotide kinase activity based on dual amplification. Biosens Bioelectron 2016; 80:91-97. [DOI: 10.1016/j.bios.2016.01.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 11/16/2022]
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Cen Y, Yang Y, Yu RQ, Chen TT, Chu X. A cobalt oxyhydroxide nanoflake-based nanoprobe for the sensitive fluorescence detection of T4 polynucleotide kinase activity and inhibition. NANOSCALE 2016; 8:8202-8209. [PMID: 27030367 DOI: 10.1039/c6nr01427e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phosphorylation of nucleic acids with 5'-OH termini catalyzed by polynucleotide kinase (PNK) is an inevitable process and has been implicated in many important cellular events. Here, we found for the first time that there was a significant difference in the adsorbent ability of cobalt oxyhydroxide (CoOOH) nanoflakes between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), which resulted in the fluorescent dye-labeled dsDNA still retaining strong fluorescence emission, while the fluorescence signal of ssDNA was significantly quenched by CoOOH nanoflakes. Based on this discovery, we developed a CoOOH nanoflake-based nanoprobe for the fluorescence sensing of T4 PNK activity and its inhibition by combining it with λ exonuclease cleavage reaction. In the presence of T4 PNK, dye-labeled dsDNA was phosphorylated and then cleaved by λ exonuclease to generate ssDNA, which could adsorb on the CoOOH nanoflakes and whose fluorescence was quenched by CoOOH nanoflakes. Due to the high quenching property of CoOOH nanoflakes as an efficient energy acceptor, a sensitive and selective sensing approach with satisfactory performance for T4 PNK sensing in a complex biological matrix has been successfully constructed and applied to the screening of inhibitors. The developed approach may potentially provide a new platform for further research, clinical diagnosis, and drug discovery of nucleotide kinase related diseases.
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Affiliation(s)
- Yao Cen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Yuan Yang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Ting-Ting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Xia Chu
- 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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Jin S, Liu H, Xia K, Ma C, He H, Wang K. Real-time monitoring of DNA methyltransferase activity using a hemimethylated smart probe. Mol Cell Probes 2016; 30:185-7. [PMID: 27039360 DOI: 10.1016/j.mcp.2016.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 01/20/2023]
Abstract
A real-time assay for DNA methyltransferase (MTase) activity has been developed. A hemimethylated smart probe is used as the substrate for DNA MTase. Cleavage of the methylated product leads to separation of fluorophore from quencher, giving a proportional increase in fluorescence. The method permits real-time monitoring of DNA methylation process and makes it easy to characterize the activity of DNA MTase. It also has the potential to screen suitable inhibitor drugs for DNA MTase.
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Affiliation(s)
- Shunxin Jin
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Haisheng Liu
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China; State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China.
| | - Hailun He
- State Key Laboratory of Medical Genetics & 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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Shi Z, Zhang X, Cheng R, Li B, Jin Y. A label-free cyclic assembly of G-quadruplex nanowires for cascade amplification detection of T4 polynucleotide kinase activity and inhibition. Analyst 2016. [PMID: 26215375 DOI: 10.1039/c5an00968e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Several fluorescence methods have been developed for sensitive detection of PNK activity based on signal amplification techniques, but they need fluorescently labeled DNA probes and superabundant assistant enzymes. We have addressed these limitations and report here a label-free and enzyme-free amplification strategy for sensitively and specifically studying PNK activity and inhibition via hybridization chain reaction (HCR). First, the phosphorylation of hairpin DNA H1 by T4 PNK makes it be specifically digested by lambda exonuclease (λ exo) from 5' to 3' direction to generate a single-stranded initiator which can successively open hairpins H2 and H3 to trigger an autonomous assembly of long DNA nanowires. Meanwhile, an intermolecular G-quadruplex is formed between H2 and H3, thereby providing fluorescence enhancement of N-methyl mesoporphyrin IX (NMM) which is a highly quadruplex-selective fluorophore. So, the PNK activity can be facilely and sensitively detected by using NMM as a signal probe which provides a low background signal to improve the overall sensitivity, resulting in the detection limit of 3.37 × 10(-4) U mL(-1). More importantly, its successful application for detecting PNK activity in a complex biological matrix and studying the inhibition effects of PNK inhibitors demonstrated that it provides a promising platform for screening PNK inhibitors as well as detecting PNK activity. Therefore, it is a highly sensitive, specific, reliable and cost-effective strategy which shows great potential for biological process research, drug discovery, and clinical diagnostics.
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Affiliation(s)
- Zhilu Shi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi'an 710062, China.
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Wang M, Mao Z, Kang TS, Wong CY, Mergny JL, Leung CH, Ma DL. Conjugating a groove-binding motif to an Ir(iii) complex for the enhancement of G-quadruplex probe behavior. Chem Sci 2016; 7:2516-2523. [PMID: 28660021 PMCID: PMC5477052 DOI: 10.1039/c6sc00001k] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 01/28/2016] [Indexed: 12/15/2022] Open
Abstract
G-quadruplex groove binder benzo[d,e]isoquinoline was linked to a Ir(iii) complex to generate a highly selective DNA probe.
In this study, the reported G-quadruplex groove binder benzo[d,e]isoquinoline was linked to a cyclometallated Ir(iii) complex to generate a highly selective DNA probe 1 that retains the favorable photophysical properties of the parent complex. The linked complex 1 showed advantages of both parent complex 2 and groove binder 3. Similar to 3, the conjugated complex 1 exhibits a superior affinity and selectivity for G-quadruplex DNA over other conformations of DNA or proteins, with the fold enhancement ratio obviously improved compared with parent complex 2. The molecular modelling revealed a groove-binding mode between complex 1 and G-quadruplex. Meanwhile 1 also possesses the prominent advantages of transition metal complex probes such as a large Stokes shift and long lifetime phosphorescence, which could be recognized in strong fluorescence media through time-resolved emission spectroscopy (TRES). We then employed 1 to develop a detection assay for AGR2, a potential cancer biomarker, as a “proof-of-principle” demonstration of the application of a linked complex for DNA-based detection in diluted fetal bovine serum. We anticipate that this conjugation method may be further employed in the development of DNA probes and have applications in label-free DNA-based diagnostic platforms.
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Affiliation(s)
- Modi Wang
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Zhifeng Mao
- 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 .
| | - Chun-Yuen Wong
- Department of Biology and Chemistry , City University of Hong Kong , 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 .
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37
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Shi Z, Zhang X, Cheng R, Zhang Q, Jin Y. High-throughout identification of telomere-binding ligands based on photo-induced electron transfer. RSC Adv 2016. [DOI: 10.1039/c5ra25612g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A fast and cost-effective method is developed for high-throughout screening G-quadruplex-binding ligands based on the photo-induced electron transfer.
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Affiliation(s)
- Zhilu Shi
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Xiafei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Rui Cheng
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Qi Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
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38
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G-Quadruplex DNAzyme Biosensor for Quantitative Detection of T4 Polynucleotide Kinase Activity by Using Split-to-intact G-Quadruplex DNAzyme Conversion. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60900-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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39
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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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40
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41
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Label-free and sensitive detection of T4 polynucleotide kinase activity via coupling DNA strand displacement reaction with enzymatic-aided amplification. Biosens Bioelectron 2015; 73:138-145. [DOI: 10.1016/j.bios.2015.05.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/05/2015] [Accepted: 05/26/2015] [Indexed: 01/04/2023]
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42
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Ma C, Liu H, Du J, Chen H, He H, Jin S, Wang K, Wang J. Quencher-free hairpin probes for real-time detection of T4 polynucleotide kinase activity. Anal Biochem 2015; 494:1-3. [PMID: 26518115 DOI: 10.1016/j.ab.2015.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/07/2015] [Accepted: 10/19/2015] [Indexed: 11/18/2022]
Abstract
Traditional methods of assaying polynucleotide kinase (PNK) activity are discontinuous, time-consuming, and laborious. Here we report a new quencher-free approach to real-time monitoring of PNK activity using a 2-aminopurine probe. When the 2-aminopurine probe was 5'-phosphorylated by PNK, it could be efficiently degraded by lambda exonuclease to release free 2-aminopurine molecules and generate a fluorescence signal. This method not only provides a universal approach to real-time monitoring of PNK activity, but also shows great potential for screening suitable inhibitor drugs for PNK.
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Affiliation(s)
- Changbei Ma
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China; State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China.
| | - Haisheng Liu
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Junyan Du
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Hanchun Chen
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Hailun He
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Shunxin Jin
- State Key Laboratory of Medical Genetics & 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
| | - Jun Wang
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
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43
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Tao M, Shi Z, Cheng R, Zhang J, Li B, Jin Y. Highly specific fluorescence detection of T4 polynucleotide kinase activity via photo-induced electron transfer. Anal Biochem 2015; 485:18-24. [PMID: 26050629 DOI: 10.1016/j.ab.2015.05.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/10/2015] [Accepted: 05/31/2015] [Indexed: 10/23/2022]
Abstract
Sensitive and reliable study of the activity of polynucleotide kinase (PNK) and its potential inhibitors is of great importance for biochemical interaction related to DNA phosphorylation as well as development of kinase-targeted drug discovery. To achieve facile and reliable detection of PNK activity, we report here a novel fluorescence method for PNK assay based on a combination of exonuclease cleavage reaction and photo-induced electron transfer (PIET) by using T4 PNK as a model target. The fluorescence of 3'-carboxyfluorescein-labeled DNA probe (FDNA) is effectively quenched by deoxyguanosines at the 5' end of its complementary DNA (cDNA) due to an effective PIET between deoxyguanosines and fluorophore. Whereas FDNA/cDNA hybrid is phosphorylated by PNK and then immediately cleaved by lambda exonuclease (λ exo), fluorescence is greatly restored due to the break of PIET. This homogeneous PNK activity assay does not require a complex design by taking advantage of the quenching ability of deoxyguanosines, making the proposed strategy facile and cost-effective. The activity of PNK can be sensitively detected in the range of 0.005 to 10 U mL(-1) with a detection limit of 2.1×10(-3) U mL(-1). Research on inhibition efficiency of different inhibitors demonstrated that it can be explored to evaluate inhibition capacity of inhibitors. The application for detection of PNK activity in complex matrix achieved satisfactory results. Therefore, this PIET strategy opens a promising avenue for studying T4 PNK activity as well as evaluating PNK inhibitors, which is of great importance for discovering kinase-targeted drugs.
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Affiliation(s)
- Mangjuan Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhilu Shi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Rui Cheng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Baoxin Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
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Zhuang J, Lai W, Xu M, Zhou Q, Tang D. Plasmonic AuNP/g-C3N4 Nanohybrid-based Photoelectrochemical Sensing Platform for Ultrasensitive Monitoring of Polynucleotide Kinase Activity Accompanying DNAzyme-Catalyzed Precipitation Amplification. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8330-8. [PMID: 25837792 DOI: 10.1021/acsami.5b01923] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A convenient and feasible photoelectrochemical (PEC) sensing platform based on gold nanoparticles-decorated g-C3N4 nanosheets (AuNP/g-C3N4) was designed for highly sensitive monitoring of T4 polynucleotide kinase (PNK) activity, using DNAzyme-mediated catalytic precipitation amplification. To realize our design, the AuNP/g-C3N4 nanohybrid was initially synthesized through in situ reduction of Au(III) on the g-C3N4 nanosheets, which was utilized for the immobilization of hairpin DNA1 (HP1) on the sensing interface. Thereafter, a target-induced isothermal amplification was automatically carried out on hairpin DNA2 (HP2) in the solution phase through PNK-catalyzed 5'-phosphorylation accompanying formation of numerous trigger DNA fragments, which could induce generation of hemin/G-quadruplex-based DNAzyme on hairpin DNA1. Subsequently, the DNAzyme could catalyze the 4-chloro-1-naphthol (4-CN) oxidation to produce an insoluble precipitation on the AuNP/g-C3N4 surface, thereby resulting in the local alternation of the photocurrent. Experimental results revealed that introduction of AuNP on the g-C3N4 could cause a ∼100% increase in the photocurrent because of surface plasmon resonance-enhanced light harvesting and separation of photogenerated e-/h+ pairs. Under the optimal conditions, the percentage of photocurrent decrement (ΔI/I0, relative to background signal) increased with the increasing PNK activity in a dynamic working range from 2 to 100 mU mL(-1) with a low detection limit (LOD) of 1.0 mU mL(-1). The inhibition effect of adenosine diphosphate also received a good performance in PNK inhibitor screening research, thereby providing a useful scheme for practical use in quantitative PNK activity assay for life science and biological research.
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45
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Miao P, Tang Y, Wang B, Yin J, Ning L. Signal amplification by enzymatic tools for nucleic acids. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.12.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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46
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Sun NN, Kong RM, Qu F, Zhang X, Zhang S, You J. An amplified fluorescence detection of T4 polynucleotide kinase activity based on coupled exonuclease III reaction and a graphene oxide platform. Analyst 2015; 140:1827-31. [DOI: 10.1039/c4an01953a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel amplified fluorescence graphene oxide (GO) sensing system for sensitive detection of T4 polynucleotide kinase (PNK) activity and inhibition was developed based on the exonuclease III (ExoIII) reaction.
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Affiliation(s)
- Ni-Na Sun
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Rong-Mei Kong
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Fengli Qu
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Xiaobing Zhang
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Shufang Zhang
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Jinmao You
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
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47
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Xu Q, Zhang Y, Zhang CY. A triple-color fluorescent probe for multiple nuclease assays. Chem Commun (Camb) 2015; 51:9121-4. [DOI: 10.1039/c5cc02177d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We develop a triple-color fluorescent probe which may function as a lab-on-a-DNA-molecule for simultaneous detection of multiple nucleases.
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Affiliation(s)
- Qinfeng Xu
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Yihong Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
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48
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Guo X, Yang X, Liu P, Wang K, Wang Q, Guo Q, Huang J, Li W, Xu F, Song C. Multiple amplification detection of microRNA based on the host–guest interaction between β-cyclodextrin polymer and pyrene. Analyst 2015; 140:4291-7. [DOI: 10.1039/c5an00626k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The proposed multiple amplification strategy based on the host–guest interaction between β-CDP and pyrene is homogeneous, sensitive and rapid.
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49
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Zhou L, Shen X, Sun N, Wang K, Zhang Y, Pei R. Label-free fluorescence light-up detection of T4 polynucleotide kinase activity using the split-to-intact G-quadruplex strategy by ligation-triggered and toehold-mediated strand displacement release. Analyst 2015; 140:5450-3. [DOI: 10.1039/c5an01032b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free, fluorescence light-up detection method for T4 polynucleotide kinase activity has been developed using the split-to-intact G-quadruplex strategy.
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Affiliation(s)
- Lu Zhou
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Na Sun
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Yuanyuan Zhang
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
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50
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Zhou F, Wang G, Shi D, Sun Y, Sha L, Qiu Y, Zhang X. One-strand oligonucleotide probe for fluorescent label-free “turn-on” detection of T4 polynucleotide kinase activity and its inhibition. Analyst 2015; 140:5650-5. [DOI: 10.1039/c5an00862j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Thioflavin T (ThT), as one of the most exciting fluorogenic molecules, boasts the “molecular-rotor” ability to induce DNA sequences containing guanine repeats to fold into G-quadruplex structures.
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Affiliation(s)
- Fu Zhou
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Guangfeng Wang
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Dongmin Shi
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Yue Sun
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Liang Sha
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Yuwei Qiu
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Xiaojun Zhang
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
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