1
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Ashrafi AM, Mukherjee A, Saadati A, Matysik FM, Richtera L, Adam V. Enhancing the substrate selectivity of enzyme mimetics in biosensing and bioassay: Novel approaches. Adv Colloid Interface Sci 2024; 331:103233. [PMID: 38924801 DOI: 10.1016/j.cis.2024.103233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
A substantial development in nanoscale materials possessing catalytic activities comparable with natural enzymes has been accomplished. Their advantages were owing to the excellent sturdiness in an extreme environment, possibilities of their large-scale production resulting in higher profitability, and easy manipulation for modification. Despite these advantages, the main challenge for artificial enzyme mimetics is the lack of substrate selectivity where natural enzymes flourish. This review addresses this vital problem by introducing substrate selectivity strategies to three classes of artificial enzymes: molecularly imprinted polymers, nanozymes (NZs), and DNAzymes. These rationally designed strategies enhance the substrate selectivity and are discussed and exemplified throughout the review. Various functional mechanisms associated with applying enzyme mimetics in biosensing and bioassays are also given. Eventually, future directives toward enhancing the substrate selectivity of biomimetics and related challenges are discussed and evaluated based on their efficiency and convenience in biosensing and bioassays.
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Affiliation(s)
- Amir M Ashrafi
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Institute of Photonics and Electronics, Czech Academy of Sciences, Prague, Czech Republic.
| | - Atripan Mukherjee
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnici 835, 252 41 Dolni Brezany, Czech Republic.
| | - Arezoo Saadati
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic.
| | - Frank-Michael Matysik
- Institute of Analytical Chemistry, Chemo- and Biosensors, University Regensburg, 93053 Regensburg, Germany.
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
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2
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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3
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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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4
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Cui W, Fan X, Zhao W, Liu J, Zheng L, Zhou L, Zhang J, Zhang X, Wang X. A label-free fluorescent biosensor for amplified detection of T4 polynucleotide kinase activity based on rolling circle amplification and catalytic hairpin assembly. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121938. [PMID: 36209712 DOI: 10.1016/j.saa.2022.121938] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/06/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
T4 polynucleotide kinase (PNK) plays a key role in maintaining genome integrity and repairing DNA damage. In this paper, we proposed a label-free fluorescent biosensor for amplified detection of T4 PNK activity based on rolling circle amplification (RCA) and catalytic hairpin assembly (CHA). Firstly, we designed a padlock probe with a 5'-hydroxyl terminus for phosphorylation reaction, a complementary sequence of the primer for initiating RCA, and a complementary sequence of the trigger for triggering CHA. T4 PNK catalyzed the phosphorylation reaction by adding a phosphate group to the 5'-hydroxyl terminus of padlock probe, generating a phosphorylated padlock probe. Then it hybridized with the primer to generate a circular probe under the action of ligase. Subsequently, the primer initiated an RCA reaction along the circular probe to synthesize a large molecular weight product with repetitive trigger sequences. The triggers then triggered the cyclic assembly reactions between hairpin probe 1 and hairpin probe 2 to generate a large amount of complexes with free G-rich sequences. The free G-rich sequences folded into G-quadruplex structures, and the N-methylmesoporphyrin IXs were inserted into them to produce an amplified fluorescent signal. Benefiting from high amplification efficiency of RCA and CHA, this fluorescent biosensor could detect T4 PNK as low as 6.63 × 10-4 U mL-1, and was successfully applied to detect its activity in HeLa cell lysates. Moreover, this fluorescent biosensor could effectively distinguish T4 PNK from other alternatives and evaluate the inhibitory effect of inhibitor, indicating that it had great potential in drug screening and disease treatment.
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Affiliation(s)
- Wanling Cui
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China.
| | - Xiaoyang Fan
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | - Wenqi Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | - Jinrong Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | | | - Libing Zhou
- Laoling People's Hospital, Dezhou 253600, PR China
| | - Junye Zhang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | - Xiumei Zhang
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, PR China
| | - Xiaoxin Wang
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, PR China
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5
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Wei L, Kong X, Wang M, Zhang Y, Pan R, Cheng Y, Lv Z, Zhou J, Ming J. A label-free T4 polynucleotide kinase fluorescence sensor based on split dimeric G-quadruplex and ligation-induced dimeric G-quadruplex/thioflavin T conformation. Anal Bioanal Chem 2022; 414:7923-7933. [PMID: 36136111 DOI: 10.1007/s00216-022-04327-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/01/2022]
Abstract
The phosphorylation process of DNA by T4 polynucleotide kinase (T4 PNK) plays a crucial role in DNA recombination, DNA replication, and DNA repair. Traditional monomeric G-quadruplex (G4) systems are always activated by single cation such as K+ or Na+. The conformation transformation caused by the coexistence of multiple cations may interfere with the signal readout and limit their applications in physiological system. In view of the stability of dimeric G4 in multiple cation solution, we reported a label-free T4 PNK fluorescence sensor based on split dimeric G4 and ligation-induced dimeric G4/thioflavin T (ThT) conformation. The dimeric G4 was divided into two independent pieces of one normal monomeric G4 and the other monomeric G4 fragment phosphorylated by T4 PNK in order to decrease the background signal. With the introduction of template DNA, DNA ligase, and invasive DNA, the dimeric G4 could be generated and liberated to combine with ThT to show obvious fluorescence signal. Using our strategy, the linear range from 0.005 to 0.5 U mL-1, and the detection limit of 0.0021 U mL-1 could be achieved without the consideration of interference caused by the coexistence of multiple cations. Additionally, research in real sample determination and inhibition effect investigations indicated its further potential application value in biochemical process research and clinic diagnostics.
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Affiliation(s)
- Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Xianglong Kong
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Mengran Wang
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yixin Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Ruiyan Pan
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yuanzheng Cheng
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Zhihua Lv
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China.
| | - Jin Zhou
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China.
| | - Jingjing Ming
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China.
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6
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A multiple primers-mediated exponential rolling circle amplification strategy for highly sensitive detection of T4 polynucleotide kinase and T4 DNA ligase activity. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Jia D, Fan W, Ren W, Liu C. One-step detection of T4 polynucleotide kinase activity based on single particle-confined enzyme reaction and digital particle counting. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Yang J, He G, Wu W, Deng W, Tan Y, Xie Q. Sensitive photoelectrochemical determination of T4 polynucleotide kinase using AuNPs/SnS 2/ZnIn 2S 4 photoactive material and enzymatic reaction-induced DNA structure switch strategy. Talanta 2022; 249:123660. [PMID: 35689947 DOI: 10.1016/j.talanta.2022.123660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 12/30/2022]
Abstract
We report here Au nanoparticles (AuNPs)/SnS2/ZnIn2S4 as a high-performance active material for sensitive photoelectrochemical (PEC) determination of T4 polynucleotide kinase (T4 PNK) using an enzymatic reaction-induced DNA structure switch strategy. To construct the PEC biosensor, a double-stranded DNA probe consisting of a CdS quantum dots (QDs)-labeled single-stranded DNA (sDNA) and its complementary DNA (cDNA) is immobilized on the AuNPs/SnS2/ZnIn2S4 photoactive material. T4 PNK can catalyze the phosphorylation of 5'-OH-terminated sDNA in the double-stranded DNA probe when ATP is present, and λ-exonuclease can catalyze the degradation of the phosphorylated sDNA into small fragments. Then the cDNA forms a hairpin structure so that CdS QDs and AuNPs are in close contact, which can induce exciton-plasma interactions between CdS QDs and AuNPs. The exciton-plasma interactions significantly boost the photocurrent, enabling the "signal on" PEC determination of T4 PNK in the range of 10-4 - 1 U mL-1 with a detection limit of 6 × 10-5 U mL-1. The PEC biosensor can also be used to screen enzyme inhibitors.
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Affiliation(s)
- Jinhua Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Guihua He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Wenying Wu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Wenfang Deng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Yueming Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China.
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
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9
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Chen F, Li G, Wu C, Wang W, Ma DL, Leung CH. A rapid and label-free DNA-based interference reduction nucleic acid amplification strategy for viral RNA detection. Biosens Bioelectron 2022; 198:113829. [PMID: 34840016 DOI: 10.1016/j.bios.2021.113829] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/11/2021] [Accepted: 11/19/2021] [Indexed: 12/26/2022]
Abstract
Common reference methods for COVID-19 diagnosis include thermal cycling amplification (e.g. RT-PCR) and isothermal amplification methods (e.g. LAMP and RPA). However, they may not be suitable for direct detection in environmental and biological samples due to background signal interference. Here, we report a rapid and label-free interference reduction nucleic acid amplification strategy (IR-NAAS) that exploits the advantages of luminescent iridium(III) probes, time-resolved emission spectroscopy (TRES) and multi-branch rolling circle amplification (mbRCA). Using IR-NAAS, we established a luminescence approach for diagnosing COVID-19 RNAs sequences RdRp, ORF1ab and N with a linear range of 0.06-6.0 × 105 copies/mL and a detection limit of down to 7.3 × 104 copies/mL. Moreover, the developed method was successfully applied to detect COVID-19 RNA sequences from various environmental and biological samples, such as domestic sewage, and mice urine, blood, feces, lung tissue, throat and nasal secretions. Apart from COVID-19 diagnosis, IR-NAAS was also demonstrated for detecting other RNA viruses, such as H1N1 and CVA10, indicating that this approach has great potential approach for routine preliminary viral detection.
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Affiliation(s)
- Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China; Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China.
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10
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Zhang X, Zhang J, Zhang Y, Zhang Y, Hou T, Wang S. Homing peptide combined with DNAzyme-based ELISA-like assay for highly specific and sensitive detection of fibrin. Talanta 2022; 238:122995. [PMID: 34857328 DOI: 10.1016/j.talanta.2021.122995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022]
Abstract
A highly sensitive and specific ELISA-like chemiluminescence method for detection of fibrin has been developed. In the sensing platform, the homing peptide (CREKA), as recognition molecule, which can specially recognize the fibrin on microtiter plate, combined with G-quadruplex-based DNAzyme to form the probe of G-quadruplex-hemin DNAzyme-CREKA. After the sample solution was coated on the plates, the probe was crosslinked with fibrin through the interaction of CREKA and fibrin. Finally, luminol-H2O2 chemiluminesecence (CL) reaction was exploited for quantitative analysis of fibrin. The liner range for fibrin detection was from 0.112 pmol L-1 to 5.6 pmol L-1 with the detection limit of fibrin as low as 0.04 pmol L-1, based on a signal-to-noise ratio (S/N) of 3. Furthermore, on the basis of the high amplification efficiency of the rolling circle amplification (RCA) reaction, the method enabled to analyze fibrin with a detection limit corresponding to 0.06 fmol L-1, whose sensitivity increased 3 orders of magnitude than that of above method in the absence of RCA reaction. In particular, combined with the separation and washing steps of ELISA, the proposed method possessed higher selectivity, high-throughput and low cost, which shows promise for applications in clinical diagnosis.
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Affiliation(s)
- Xifang Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Jinrong Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Yuanfu Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China.
| | - Yinghong Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Tingting Hou
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Shuhao Wang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China.
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11
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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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12
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Han Y, Liu X, Zhao Q, Gao Y, Zhou D, Long W, Wang Y, Song Y. Aptazyme-induced cascade amplification integrated with a volumetric bar-chart chip for highly sensitive detection of aflatoxin B1 and adenosine triphosphate. Analyst 2022; 147:2500-2507. [DOI: 10.1039/d2an00650b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A triple-channel volumetric bar-chart chip based on aptazyme-induced cascade signal amplification empowers visual readout of aflatoxin B1 and adenosine triphosphate concentration.
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Affiliation(s)
- Yuanyue Han
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Xinli Liu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Qiao Zhao
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yanfeng Gao
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Dongtao Zhou
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Wenxiu Long
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yuzhen Wang
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yujun Song
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
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13
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Liu T, Li Z, Chen M, Zhao H, Zheng Z, Cui L, Zhang X. Sensitive electrochemical biosensor for Uracil-DNA glycosylase detection based on self-linkable hollow Mn/Ni layered doubled hydroxides as oxidase-like nanozyme for cascade signal amplification. Biosens Bioelectron 2021; 194:113607. [PMID: 34507096 DOI: 10.1016/j.bios.2021.113607] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/29/2021] [Indexed: 02/06/2023]
Abstract
Nanozymes have been widely used in biosensors instead of natural enzymes because of low cost, high stability and ease of storage. However, few works use oxidase-like nanozymes to fabricate electrochemical biosensors. Herein, we proposed a sensitive electrochemical biosensor to detect uracil-DNA glycosylase (UDG) based on the hollow Mn/Ni layered doubled hydroxides (h-Mn/Ni LDHs) as oxidase-like nanozyme. Briefly, the h-Mn/Ni LDHs, which was prepared by a facile hydrothermal method, exhibited excellent oxidase-like activity because the hollow structure provided rich active sites and high specific surface area. Then, the signal probes were constructed by assembling the hairpin DNA (hDNA), single DNA1 and DNA2 on the h-Mn/Ni LDHs, respectively. In the presence of UDG, the uracil bases in the stem of hDNA were specifically excised, generating apyrimidinic (AP) sites and inducing the unwinding of the hDNA. Afterwards, the h-Mn/Ni LDHs@Au-hDNA/DNA1 was connected on the electrode via hybridization between unwinded hDNA and capture DNA (cDNA). Subsequently, the self-linking process allowed the retention of numerous h-Mn/Ni LDHs through simple DNA hybridization to amplify the signal of o-phenylenediamine (o-PD). Unlike many peroxidase-like nanozyme-based electrochemical biosensors, there is no need to add H2O2 during the experimental process, which effectively reduced the background signal as well as improved the stability of the biosensor. As expected, the biosensor exhibited excellent performance with a wide linear range and a low detection limit. This work highlights an appealing opportunity to develop a no H2O2 platform based on h-Mn/Ni LDHs for future application in biological analysis and clinical diagnosis.
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Affiliation(s)
- Tingting Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Zhiwen Li
- School of Chemistry and Pharmaceutical Engineering, Shandong First Medical University & Shandong Academy of Medical Science, Taian, 271016, PR China
| | - Mohan Chen
- Jinan Foreign Language School, Jinan, Shandong Province, 250353, China
| | - Huijuan Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Zekun Zheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong, 250014, China.
| | - Xiaomei Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China.
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14
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Li H, Warden AR, Su W, He J, Zhi X, Wang K, Zhu L, Shen G, Ding X. Highly sensitive and portable mRNA detection platform for early cancer detection. J Nanobiotechnology 2021; 19:287. [PMID: 34565398 PMCID: PMC8474757 DOI: 10.1186/s12951-021-01039-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/13/2021] [Indexed: 01/05/2023] Open
Abstract
Pancreatic cancer, at unresectable advanced stages, presents poor prognoses, which could be prevented by early pancreatic cancer diagnosis methods. Recently, a promising early-stage pancreatic cancer biomarker, extracellular vesicles (EVs) related glypican-1 (GPC1) mRNA, is found to overexpress in pancreatic cancer cells. Current mRNA detection methods usually require expensive machinery, strict preservation environments, and time-consuming processes to guarantee detection sensitivity, specificity, and stability. Herein, we propose a novel two-step amplification method (CHAGE) via the target triggered Catalytic Hairpin Assembly strategy combined with Gold-Enhanced point-of-care-testing (POCT) technology for sensitive visual detection of pancreatic cancer biomarker. First, utilizing the catalyzed hairpin DNA circuit, low expression of the GPC1 mRNA was changed into amplification product 1 (AP1, a DNA duplex) as the next detection targets of the paper strips. Second, the AP1 was loaded onto a lateral flow assay and captured with the gold signal nanoparticles to visualize results. Finally, the detected results can be further enhanced by depositing gold to re-enlarge the sizes of gold nanoparticles in detection zones. As a result, the CHAGE methodology lowers the detection limit of mRNA to 100 fM and provides results within 2 h at 37 °C. Furthermore, we demonstrate the successful application in discriminating pancreatic cancer cells by analyzing EVs' GPC1 mRNA expression levels. Hence, the CHAGE methodology proposed here provides a rapid and convenient POCT platform for sensitive detection of mRNAs through unique probes designs (COVID, HPV, etc.).
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Affiliation(s)
- Hongxia Li
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Antony R Warden
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenqiong Su
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jie He
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiao Zhi
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kan Wang
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Laikuan Zhu
- Department of Endodontics and Operative Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, 200030, China.
| | - Guangxia Shen
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China.
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15
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Zhang Q, Yang T, Zheng G, Gao H, Yan C, Zheng X, Zhou X, Shao Y. Characterization of intermolecular G-quadruplex formation over intramolecular G-triplex for DNA containing three G-tracts. Analyst 2021; 145:4254-4259. [PMID: 32478785 DOI: 10.1039/d0an00791a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-triplex (G3) has been recognized as a popular intermediate during the folding of G-quadruplex (G4). This has raised interest to anticipate the ultimate formation of G3 by shortening the G4-forming oligonucleotides with the remaining three G-tracts. Some G3 structures have been validated and their stability has been found to be affected by the loop sequences similar to G4s. In this work, however, we first found that an intermolecular parallel G4 structure was preferred in K+ for the oligonucleotide 5'-TGGGTAGGGCGGG-3' (DZ3) containing only three G-tracts. We screened auramine O (AO) as the appropriate fluorophore with a molecular rotor feature to target this G4 structure. AO bound with DZ3 in a 1 : 4 ratio, as confirmed by isothermal titration calorimetry experiments, suggesting the formation of a tetramolecular G4 structure (4erG4). The excimer emission from the labelled pyrene and the DNA melting behavior at various pHs in the presence of Ag+ proved the formation of the 4erG4 structure rather than the prevalent intramolecular G3 folding. This work demonstrates that one should be cautious while putatively predicting a G3 structure from an oligonucleotide containing three G-tracts.
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Affiliation(s)
- Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Guoxiang Zheng
- Undergraduate Teaching Department, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Xiong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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16
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Wang W, Peng Y, Wu J, Zhang M, Li Q, Zhao Z, Liu M, Wang J, Cao G, Bai J, Gao Z. Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification. Anal Chem 2021; 93:4488-4496. [PMID: 33651609 DOI: 10.1021/acs.analchem.0c04681] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
17β-Estradiol (E2) can cause an adverse effect on the human endocrine system even at the nanomolar level. Measurements of very low levels of E2 remain a critical challenge due to insufficient sensitivity. In this study, a multistep isothermal amplification fluorescence strategy was constructed, which could realize the exponential amplification of target E2. Specifically, strand displacement reaction (SDA), rolling circle amplification (RCA), and multiprimed rolling circle amplification (MRCA) were combined in a series to quantify trace complementary strand of E2 (cDNA). The E2 aptamer and cDNA were hybridized and modified on the magnetic beads. E2 could bind to its aptamer and cause the release of the cDNA. Then, cDNA would combine with the template DNA, initiating the SDA-RCA-MRCA. The molecular beacons, possessing low background signal, whose fluorescence was quenched in the state of chain folding, could be specifically recognized by the long single-stranded DNA (L-ssDNA) generated by the multistep isothermal amplification triggered by cDNA, and then the fluorescence of the molecular beacons could be restored. Therefore, the E2 could be quantitatively detected by the recovery fluorescence intensity. The fluorescence value showed a good linear relationship with the concentration of E2 in the range of 0.001836-183.6 nM, and the limit of detection (LOD) was as low as 63.09 fM. In addition, the recovery rates of this method spiked in milk and water were 80.8-107.0%, respectively. This method has the advantage of multistep isothermal amplification to obtain abundant fluorescence signals, which may provide a new possibility for highly sensitive detection of other small-molecule targets.
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Affiliation(s)
- Weiya Wang
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Jin Wu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Man Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Qiaofeng Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Zunquan Zhao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Mingzhu Liu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Jiu Wang
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China
| | - Gaofang Cao
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Zhixian Gao
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
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17
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Khan P, Aufdembrink LM, Engelhart AE. Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings. ACS Synth Biol 2020; 9:2861-2880. [PMID: 32966744 PMCID: PMC7552996 DOI: 10.1021/acssynbio.0c00359] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, poses grave threats to both the global economy and health. The predominant diagnostic screens in use for SARS-CoV-2 detection are molecular techniques such as nucleic acid amplification tests. In this Review, we compare current and emerging isothermal diagnostic methods for COVID-19. We outline the molecular and serological techniques currently being used to detect SARS-CoV-2 infection, past or present, in patients. We also discuss ongoing research on isothermal techniques, CRISPR-mediated detection assays, and point-of-care diagnostics that have potential for use in SARS-CoV-2 detection. Large-scale viral testing during a global pandemic presents unique challenges, chief among them the simultaneous need for testing supplies, durable equipment, and personnel in many regions worldwide, with each of these regions possessing testing needs that vary as the pandemic progresses. The low-cost isothermal technologies described in this Review provide a promising means by which to address these needs and meet the global need for testing of symptomatic individuals as well as provide a possible means for routine testing of asymptomatic individuals, providing a potential means of safely enabling reopenings and early monitoring of outbreaks.
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Affiliation(s)
- Pavana Khan
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| | - Lauren M. Aufdembrink
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
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18
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Wang DX, Wang J, Du YC, Ma JY, Wang SY, Tang AN, Kong DM. CRISPR/Cas12a-based dual amplified biosensing system for sensitive and rapid detection of polynucleotide kinase/phosphatase. Biosens Bioelectron 2020; 168:112556. [DOI: 10.1016/j.bios.2020.112556] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022]
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19
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Lin M, Wan H, Zhang J, Wang Q, Hu X, Xia F. Electrochemical DNA Sensors Based on MoS 2-AuNPs for Polynucleotide Kinase Activity and Inhibition Assay. ACS APPLIED MATERIALS & INTERFACES 2020; 12:45814-45821. [PMID: 32877162 DOI: 10.1021/acsami.0c13385] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The determination of T4 polynucleotide kinase (PNK) activity and the screening of PNK inhibitors are critical to disease diagnosis and drug discovery. Numerous electrochemical strategies have been developed for the sensitive measurement of PNK activity and inhibition. However, they often suffer from additional labels and multiple steps of the detection process for the electrochemical readout. Herein, we have demonstrated an electrochemical DNA (E-DNA) sensor for the one-step detection of PNK with "signal-on" readout with no need for additional labels. In our design, the highly switchable double-stranded DNA (dsDNA) probes are immobilized on the gold nanoparticle-decorated molybdenum disulfide nanomaterial (MoS2-AuNPs), which possesses large surface area and high conductivity for elevating the signal gain in the PNK detection. This signal-on E-DNA sensor integrated with MoS2-AuNPs exhibits a much higher sensitivity than that without MoS2-AuNPs, showing a detection limit of 2.18 × 10-4 U/mL. Furthermore, this assay shows high selectivity, with the ability to discriminate PNK from other enzymes and proteins, and can be utilized to screen inhibitors. The proposed sensor is easy to operate with one-step readout and robust for PNK detection in the biological matrix and shows great potential for point-of-care in clinical diagnostics and drug screening.
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Affiliation(s)
- Meihua Lin
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hao Wan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jian Zhang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Quan Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xinyu Hu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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20
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Mao J, Chen X, Xu H, Xu X. DNAzyme-driven DNA walker biosensor for amplified electrochemical detection of T4 polynucleotide kinase activity and inhibition. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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Zhao H, Yan Y, Chen M, Hu T, Wu K, Liu H, Ma C. Exonuclease III-assisted signal amplification strategy for sensitive fluorescence detection of polynucleotide kinase based on poly(thymine)-templated copper nanoparticles. Analyst 2020; 144:6689-6697. [PMID: 31598619 DOI: 10.1039/c9an01659g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A sensitive and label-free fluorometric method has been developed for the determination of polynucleotide kinase (PNK) activity, by employing exonuclease III (Exo III)-assisted cyclic signal amplification and poly(thymine)-templated copper nanoparticles (polyT-CuNPs). In the presence of PNK, cDNA with 5'-hydroxyl termini was phosphorylated and then hybridized with tDNA to form the cDNA/tDNA duplex, which subsequently triggered the λ exonuclease cleavage reaction, eventually resulting in the release of tDNA. The released tDNA could unfold the hairpin structure of HP DNA to generate partially complementary duplex (tDNA/HP DNA), wherein the HP DNA possessed T-rich sequences (T30) and tDNA recognition sequence. With the help of Exo III digestion, the tDNA was able to initiate the cycle for the generation of T-rich sequences, the template for the formation of fluorescent CuNPs. Conversely, the cDNA could not be cleaved by λ exonuclease without PNK and individual HP DNA could not be hydrolyzed by Exo III. The T-rich sequence was caged in HP DNA, resulting in a weak fluorescence signal. Under optimized conditions, the fluorescence intensity was linearly correlated to a concentration range of 0.001 to 1 U mL-1 with a low detection limit of 2 × 10-4 U mL-1. Considering the intriguing analytical performance, this approach could be explored to screen T4 PNK inhibitors and hold promising applications in drug discovery and disease therapy.
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Affiliation(s)
- Han Zhao
- School of Life Sciences, Central South University, Changsha 410013, China.
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22
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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23
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A nanoplatform based on metal-organic frameworks and coupled exonuclease reaction for the fluorimetric determination of T4 polynucleotide kinase activity and inhibition. Mikrochim Acta 2020; 187:243. [PMID: 32206934 DOI: 10.1007/s00604-020-4194-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
A nanoplatform based on metal-organic frameworks (MOFs) and lambda exonuclease (λ exo) for the fluorimetric determination of T4 polynucleotide kinase (T4 PNK) activity and inhibition is described. Fe-MIL-88 was selected as the nanomaterial because of its significant preferential binding ability to single-stranded DNA (ssDNA) over double-stranded DNA (dsDNA) and its quenching property. The synthesized Fe-MIL-88 was characterized by transmission electron microscope, scanning electron microscope, and X-ray photoelectron spectroscopy. In the presence of T4 PNK, FAM-labeled dsDNA (FAM-dsDNA) is phosphorylated on its 5'-terminal. λ exo then recognizes and cleaves the phosphorylated strand yielding FAM-labeled ssDNA (FAM-ssDNA). The fluorescence of the produced FAM-ssDNA is quenched due to Fe-MIL-88's absorbing on FAM-ssDNA. On the contrary, in the absence of T4 PNK, the phosphorylation and cleavage processes cannot take place. Therefore, the fluorescence of FAM-dsDNA still remains. The fluorescence intensity is detected at the maximum emission wavelength of 524 nm using the maximum excitation wavelength of 488 nm. The assay of T4 PNK based on the fluorescence quenching of FAM-ssDNA achieves a linear relationship in the range 0.01-5.0 U mL-1 with a detection limit of 0.0089 U mL-1 in buffer. The assay exhibits excellent performance for T4 PNK activity determination in a complex biological matrix. The results also reveal the ability of the assay for T4 PNK inhibitor screening. Graphical abstract Schematic presentation of a nanoplatform based on Fe-MIL-88 and coupled exonuclease reaction for the fluorimetric determination of T4 polynucleotide kinase activity. FAM-ssDNA, FAM-labeled single-stranded DNA; cDNA, complementary DNA; λ exo, lambda exonuclease;T4 PNK, T4 polynucleotide kinase.
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24
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Yu Y, Zhang Q, Fei Y, Yan C, Ye T, Gao L, Gao H, Zhou X, Shao Y. Multicolorfully probing intramolecular G-Quadruplex tandem interface. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117655. [PMID: 31670046 DOI: 10.1016/j.saa.2019.117655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
A long guanine-rich oliogonucleotide sequence can form multiple G-quadruplex (G4) tandem individuals in a single molecule with internal G4-G4 (inG4-G4) interfaces. The interface can exist at the stacked (s-inG4-G4) or unstacked (us-inG4-G4) state, dependent of the G4 conformation and environment. Because of the vital bioactivity of the G4 interface state, there is a great demand for developing a reliable multicolor fluorescence method to identify the interface state using a fluorophore that can emit at the individual wavelength for a specific interface. Herein, we found that a porphyrin with four dihydroxyphenyl substituents (OH2PP) can multicolorfully recognize the s-inG4-G4 dimer interface against the us-inG4-G4 dimer one. The s-inG4-G4 dimer cause significant red shifts in the excitation and emission bands of OH2PP in contrast to the us-inG4-G4 dimer and G4 monomers. OH2PP adopts a 1:1 binding mode with the s-inG4-G4 dimer, whereas a 2:1 binding mode occurs to the us-inG4-G4 dimer. The limit of detection (LOD) for the s-inG4-G4 structure is about tens of nM level. The observed binding dependence of OH2PP on the linker length between the G4 individuals suggests the interface binding with the s-inG4-G4 dimer. Deformation of the porphyrin macrocycle within the s-inG4-G4 interface confinement most likely contributes to the multicolorful response with the hyperporphyrin effect. Our work demonstrates that OH2PP is a promising fluorophore to fluorescently recognize the G4 multimer with an ideal interface-sensitive multicolor response.
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Affiliation(s)
- Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China.
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25
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Li XY, Cui YX, Du YC, Tang AN, Kong DM. Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase. Analyst 2020; 145:3742-3748. [DOI: 10.1039/c9an02569c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.
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Affiliation(s)
- 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
| | - 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
| | - 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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26
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Du YC, Wang SY, Li XY, Wang YX, Tang AN, Kong DM. Terminal deoxynucleotidyl transferase-activated nicking enzyme amplification reaction for specific and sensitive detection of DNA methyltransferase and polynucleotide kinase. Biosens Bioelectron 2019; 145:111700. [DOI: 10.1016/j.bios.2019.111700] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022]
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27
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Electrochemical detection of T4 polynucleotide kinase based on target-assisted ligation reaction coupled with silver nanoparticles. Anal Chim Acta 2019; 1085:85-90. [DOI: 10.1016/j.aca.2019.07.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 11/20/2022]
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Safarpour H, Dehghani S, Nosrati R, Zebardast N, Alibolandi M, Mokhtarzadeh A, Ramezani M. Optical and electrochemical-based nano-aptasensing approaches for the detection of circulating tumor cells (CTCs). Biosens Bioelectron 2019; 148:111833. [PMID: 31733465 DOI: 10.1016/j.bios.2019.111833] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
More recently, detection of circulating tumor cells (CTCs) has been considered as an appealing prognostic and diagnostic approach for cancer patients. CTCs as a type of tumor-derived cells are secreted by the tumor and released into the blood circulation. Since the migration of CTCs is an early event in cancer progression, patients who still have tumor-free lymph nodes have to be well examined for the CTCs presence in their blood circulation. Nowadays, there is a broad range of detection methods available to identify CTCs. As artificial RNA oligonucleotides or single-stranded DNA with receptor and catalytic characteristics, aptamers have been standing out, owing to their target-induced conformational modifications, elevated stability, and target specificity to be implemented in biosensing techniques. To date, several sensitivity-enhancement methods alongside smart nanomaterials have been used for the creation of new aptasensors to address the limit of detection (LOD), and improve the sensitivity of numerous analyte identification methods. The present review article supports a focused overview of the recent studies in the identification and quantitative determination of CTCs by aptamer-based biosensors and nanobiosensors.
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Affiliation(s)
- Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Sadegh Dehghani
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nozhat Zebardast
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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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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31
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Ultrasensitive DNA biosensor based on electrochemical atom transfer radical polymerization. Biosens Bioelectron 2019; 131:193-199. [DOI: 10.1016/j.bios.2018.11.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/31/2018] [Accepted: 11/18/2018] [Indexed: 02/04/2023]
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32
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Chen Z, Xiong F, Yu A, Lai G. Aptamer biorecognition-triggered DNAzyme liberation and Exo III-assisted target recycling for ultrasensitive homogeneous colorimetric bioassay of kanamycin antibiotic. Chem Commun (Camb) 2019; 55:3959-3962. [PMID: 30874255 DOI: 10.1039/c8cc10107h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A novel peroxidase-mimicking DNAzyme-based colorimetric homogenous bioassay is developed for kanamycin detection. Aptamer biorecognition triggers DNAzyme liberation from DNA duplexes for "off-on" signal transduction. The special hairpin structure of the aptamer-kanamycin biocomposite enables Exo III-assisted target recycling for signal amplification.
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Affiliation(s)
- Zhichao Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi 435002, P. R. China.
| | - Feng Xiong
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi 435002, P. R. China.
| | - Aimin Yu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi 435002, P. R. China. and Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn VIC 3122, Australia
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi 435002, P. R. China.
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33
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Li PP, Cao Y, Mao CJ, Jin BK, Zhu JJ. TiO2/g-C3N4/CdS Nanocomposite-Based Photoelectrochemical Biosensor for Ultrasensitive Evaluation of T4 Polynucleotide Kinase Activity. Anal Chem 2018; 91:1563-1570. [DOI: 10.1021/acs.analchem.8b04823] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Pan-Pan Li
- Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue Cao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Chang-Jie Mao
- Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, P. R. China
| | - Bao-Kang Jin
- Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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34
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Zhang X, Liu Q, Jin Y, Li B. Determination of the activity of T4 polynucleotide kinase phosphatase by exploiting the sequence-dependent fluorescence of DNA-templated copper nanoclusters. Mikrochim Acta 2018; 186:3. [DOI: 10.1007/s00604-018-3102-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/16/2018] [Indexed: 12/23/2022]
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35
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Cui L, Hu J, Li CC, Wang CM, Zhang CY. An electrochemical biosensor based on the enhanced quasi-reversible redox signal of prussian blue generated by self-sacrificial label of iron metal-organic framework. Biosens Bioelectron 2018; 122:168-174. [DOI: 10.1016/j.bios.2018.09.061] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/25/2022]
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36
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Lee IJ, Goo NI, Kim DE. Label/quencher-free detection of single-nucleotide changes in DNA using isothermal amplification and G-quadruplexes. Analyst 2018; 141:6503-6506. [PMID: 27827492 DOI: 10.1039/c6an01600f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report an analytical method that exploits the interaction between G-quadruplexes and thioflavin T (ThT), for detecting mutant DNA species containing single-base changes. This system is a label/quencher-free fluorescence enhancement system based on rolling circle amplification (RCA)-responsive G-quadruplex formation, which enables a highly selective detection of T790M SNPs in the gene encoding the epidermal growth factor receptor, EGFR.
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Affiliation(s)
- Il Joon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
| | - Nam-In Goo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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37
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Cui L, Hu J, Wang M, Diao XK, Li CC, Zhang CY. Mimic Peroxidase- and Bi2S3 Nanorod-Based Photoelectrochemical Biosensor for Signal-On Detection of Polynucleotide Kinase. Anal Chem 2018; 90:11478-11485. [DOI: 10.1021/acs.analchem.8b02673] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- 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
| | - Juan Hu
- 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
| | - Meng 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
| | - Xing-kang Diao
- 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
| | - Chen-chen 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
| | - 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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38
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Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing. Pharmaceuticals (Basel) 2018; 11:E35. [PMID: 29690513 PMCID: PMC6027247 DOI: 10.3390/ph11020035] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.
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Affiliation(s)
- Lide Gu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Wanli Yan
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Le Liu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Shujun Wang
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Xu Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
- Verschuren Centre for Sustainability in Energy & the Environment, Cape Breton University, Sydney, NS B1P 6L2, Canada.
| | - Mingsheng Lyu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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39
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Norouzi A, Ravan H, Mohammadi A, Hosseinzadeh E, Norouzi M, Fozooni T. Aptamer-integrated DNA nanoassembly: A simple and sensitive DNA framework to detect cancer cells. Anal Chim Acta 2018. [PMID: 29534792 DOI: 10.1016/j.aca.2018.02.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals. As proof-of-concept, as low as 175 cancer cells were detected by the assay, and color change was clearly distinguished by the naked eyes. The proposed system enjoys potential applications for point-of-care cancer diagnosis, with its excellent sensitivity and selectivity.
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Affiliation(s)
- Akram Norouzi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Abbas Mohammadi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Elyas Hosseinzadeh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahdieh Norouzi
- Department of Nursing, Islamic Azad University of Kerman, Kerman, Iran
| | - Tahereh Fozooni
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
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40
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Feng C, Wang Z, Chen T, Chen X, Mao D, Zhao J, Li G. A Dual-Enzyme-Assisted Three-Dimensional DNA Walking Machine Using T4 Polynucleotide Kinase as Activators and Application in Polynucleotide Kinase Assays. Anal Chem 2018; 90:2810-2815. [DOI: 10.1021/acs.analchem.7b04924] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chang Feng
- State
Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation
Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P.R. China
| | - Zihan Wang
- Center
for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Tianshu Chen
- Center
for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Xiaoxia Chen
- Center
for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Dongsheng Mao
- Center
for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Jing Zhao
- Center
for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Genxi Li
- State
Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation
Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P.R. China
- Center
for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
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41
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Li XY, Du YC, Pan YN, Su LL, Shi S, Wang SY, Tang AN, Kim K, Kong DM. Dual enzyme-assisted one-step isothermal real-time amplification assay for ultrasensitive detection of polynucleotide kinase activity. Chem Commun (Camb) 2018; 54:13841-13844. [DOI: 10.1039/c8cc08616h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A novel, simple, one-step and one-tube detection method for polynucleotide kinase (PNK) activity based on isothermal real-time amplification assay was proposed.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Yan-Nian Pan
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Li-Li Su
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Shuo Shi
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Si-Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Kwangil Kim
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
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42
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Cui L, Li Y, Lu M, Tang B, Zhang CY. An ultrasensitive electrochemical biosensor for polynucleotide kinase assay based on gold nanoparticle-mediated lambda exonuclease cleavage-induced signal amplification. Biosens Bioelectron 2018; 99:1-7. [DOI: 10.1016/j.bios.2017.07.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 12/24/2022]
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43
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Peng H, Newbigging AM, Wang Z, Tao J, Deng W, Le XC, Zhang H. DNAzyme-Mediated Assays for Amplified Detection of Nucleic Acids and Proteins. Anal Chem 2017; 90:190-207. [DOI: 10.1021/acs.analchem.7b04926] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hanyong Peng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Ashley M. Newbigging
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Wenchan Deng
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental
Toxicology, Department of Laboratory Medicine and Pathology, Faculty
of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
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44
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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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45
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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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46
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Li XY, Du YC, Zhang YP, Kong DM. Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Sci Rep 2017; 7:6263. [PMID: 28740223 PMCID: PMC5524717 DOI: 10.1038/s41598-017-06594-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/14/2017] [Indexed: 12/31/2022] Open
Abstract
An exonucleolytic digestion-assisted exponential rolling circle amplification (RCA) strategy was developed for sensitive and sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Herein, Phi29 DNA polymerase plays two important roles as exonuclease and polymerase. Long-stranded genomic DNAs can be broken into small DNA fragments after ultrasonication. The fragments that contain target DNA, hybridize with a linear padlock probe to trigger the formation of a circular RCA template. The tails protruding from the 3'-end of the target DNA sequences are then digested by the 3' → 5' exonuclease activity of Phi29 DNA polymerase even if they fold into a double-stranded structure. The digested DNA fragments can then initiate subsequent RCA reaction. RCA products, which are designed to fold into G-quadruplex structures, exponentially accumulate when appropriate nicking endonuclease recognition sites are introduced rationally into the RCA template. This method is demonstrated to work well for real genomic DNA detection using human pathogen Cryptococcus neoformans as a model. In addition, this work has two other important discoveries: First, the presence of a 3'-tail can protect the RCA primer from degradation by Phi29 DNA polymerase. Second, 3' → 5' exonucleolytic activity of Phi29 DNA polymerase can work for both single- and double-stranded DNA.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P.R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Yi-Chen Du
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Yu-Peng Zhang
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P.R. China.
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300071, P.R. China.
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47
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Harkness RW, Mittermaier AK. G-quadruplex dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28642152 DOI: 10.1016/j.bbapap.2017.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Robert W Harkness
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada
| | - Anthony K Mittermaier
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada.
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48
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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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49
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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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50
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Label-free fluorescent assay of T4 polynucleotide kinase phosphatase activity based on G-quadruplexe−thioflavin T complex. Talanta 2017; 165:653-658. [DOI: 10.1016/j.talanta.2017.01.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/27/2016] [Accepted: 01/06/2017] [Indexed: 02/06/2023]
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