1
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Chen R, Cao Y, Liu Y, Zhao D, Li J, Cheng Z, Bi C, Zhang X. Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65. Nat Commun 2023; 14:257. [PMID: 36650182 PMCID: PMC9845348 DOI: 10.1038/s41467-023-35919-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Prime editing is a versatile gene editing tool that enables precise sequence changes of all types in the genome, but its application is rather limited by the editing efficiency. Here, we first apply the Suntag system to recruit the transcription factor P65 and enhance the desired editing outcomes in the prime editing system. Next, MS2 hairpins are used to recruit MS2-fused P65 and confirmed that the recruitment of the P65 protein could effectively improve the prime editing efficiency in both the PE3 and PE5 systems. Moreover, this suggests the increased editing efficiency is most likely associated with the induction of chromatin accessibility change by P65. In conclusion, we apply different systems to recruit P65 and enhance the prime editing efficiency of various PE systems. Furthermore, our work provides a variety of methods to work as protein scaffolds for screening target factors and thus supports further optimization of prime editing systems.
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Affiliation(s)
- Ronghao Chen
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Cao
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yajing Liu
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Zhihui Cheng
- College of Life Science, Nankai University, Tianjin, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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2
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Self-assembled Nanosheets of Perylene Monoamide Derivative as Sensitive Fluorescent Biosensor for Exonuclease III Activity. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Li X, Falcone N, Hossain MN, Kraatz HB, Chen X, Huang H. Development of a novel label-free impedimetric electrochemical sensor based on hydrogel/chitosan for the detection of ochratoxin A. Talanta 2021; 226:122183. [PMID: 33676715 DOI: 10.1016/j.talanta.2021.122183] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 01/15/2023]
Abstract
Ochratoxin A (OTA) is one of the most abundant mycotoxins that contaminate various food products. Herein, we propose a novel label-free impedimetric electrochemical sensor consisting of chitosan/dipeptide nanofibrous hydrogel and immobilized DNA probes with OTA aptamer for the detection of OTA. The thin film of chitosan/dipeptide nanofibrous hydrogel was used as sensing interface and carrier for hybridization chain reaction (HCR) of OTA aptamer and DNA2 strand to form DNA concatemer. The concatemer was dissociated to single-stranded DNA (ssDNA) in the presence of target OTA, and the signal amplification was further implemented by introducing RecJf exonuclease, which could digest the single-stranded DNA resulting in OTA recycle. Electrochemical impedance spectroscopy (EIS) has been employed to characterize the properties of the fabricated sensor. A linear detection range of 0.1-100 ng mL-1 was obtained for OTA with a low detection limit of 0.03 ng mL-1. Furthermore, the developed sensor was demonstrated in white wine to detect OTA, indicating that the proposed impedimetric sensor has a promising potential application in the food industry.
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Affiliation(s)
- Xiaoyan Li
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, PR China; College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China
| | - Natashya Falcone
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1065 Military Trail, Toronto, ON M1C 1A4, Canada
| | - M Nur Hossain
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1065 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1065 Military Trail, Toronto, ON M1C 1A4, Canada.
| | - Xiaojun Chen
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China.
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, PR China; School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, PR China.
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4
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Kim DM, Yoo SM. DNA-modifying enzyme reaction-based biosensors for disease diagnostics: recent biotechnological advances and future perspectives. Crit Rev Biotechnol 2020; 40:787-803. [DOI: 10.1080/07388551.2020.1764485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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5
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Liu X, Wu Y, Wu X, Zhao JX. A graphene oxide-based fluorescence assay for the sensitive detection of DNA exonuclease enzymatic activity. Analyst 2020; 144:6231-6239. [PMID: 31552930 DOI: 10.1039/c9an01283d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The 3'-5' exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π-π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3'-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an inefficient fluorescence quenching. As a result, the fluorescence intensity of the sensor was found to be proportional to the concentration of Exo III; towards the detection of Exo III, this simple GO-based probe demonstrated a highly sensitive and selective linear response in the low detection range from 0.01 U mL-1 to 0.5 U mL-1 and with the limit of detection (LOD) of 0.001 U mL-1. Compared with other fluorescent probes, this assay exhibited superior sensitivity and selectivity in both buffer and fetal bovine serum samples, in addition to being cost effective and having a simple setup.
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Affiliation(s)
- Xiao Liu
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202, USA.
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6
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Burkin KM, Bodulev OL, Gribas AV, Sakharov IY. One-step label-free chemiluminescent assay for determination of exonuclease III activity towards hairpin oligonucleotides. Enzyme Microb Technol 2019; 131:109419. [PMID: 31615661 DOI: 10.1016/j.enzmictec.2019.109419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023]
Abstract
Fast label-free chemiluminescent assay for determination of exonuclease III (ExoIII) activity measured towards hairpin oligonucleotide substrates was developed. The designed substrates consisted of EAD2 aptamer to hemin which was associated with DNA sequence complementary to 5'-terminus fragment of EAD2. In the presence of ExoIII the associated sequence of the hairpin stem was digested, producing EAD2 aptamer which reacted with hemin with the formation of peroxidase-mimicking DNAzyme (PMDNAzyme). The catalytic activity of the produced PMDNAzyme was measured towards luminol/H2O2. Under the optimized conditions the limit of detection and sensitivity of the one-step chemiluminescent assay of ExoIII were 7.3 nM and 1.7 × 108 M-1, respectively. The coefficient of variation (CV) was lower than 6%.
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Affiliation(s)
- Konstantin M Burkin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia
| | - Oleg L Bodulev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia
| | - Anastasia V Gribas
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia.
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7
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Ding Y, Li X, Zhang X, Li F, Hou X, Wu P. Systematic Probing of the Sequence Selectivity of Exonuclease III with a Photosensitization Colorimetric Assay. ACS OMEGA 2019; 4:13382-13387. [PMID: 31460466 PMCID: PMC6705212 DOI: 10.1021/acsomega.9b01560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Exonuclease III (Exo III) is an important enzymatic tool that is being widely used in molecular biology, biotechnology, and bioassay development. Exo III prefers to cleave double-stranded DNA (dsDNA) with blunt and recessed 3'-termini rather than their protruding counterpart. While it has been accepted that a short 3'-overhang (e.g., >4 nt) is necessary to protect a dsDNA from Exo III cleavage, critical roles of the length and sequence of this 3'-overhang remain unexplored. Herein, we develop a novel light-induced colorimetric assay allowing the systematic probe of the sequence selectivity of Exo III in a rapid and high-throughput manner. Our finding that Exo III is highly specific to 3'-overhang in terms of both length and sequence will be valuable for guiding the design of bioassays and DNA manipulating tools mediated by Exo III.
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Affiliation(s)
- Yu Ding
- Analytical
& Testing Center, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xianming Li
- Analytical
& Testing Center, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xinfeng Zhang
- College
of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Feng Li
- Analytical
& Testing Center, College of Chemistry, Sichuan University, Chengdu 610064, China
- Department
of Chemistry, Center for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Xiandeng Hou
- Analytical
& Testing Center, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Peng Wu
- Analytical
& Testing Center, College of Chemistry, Sichuan University, Chengdu 610064, China
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8
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Hu W, Zhao H, Jing J, Zhang X. A label-free ratiometric fluorescence strategy for 3′–5′ exonuclease detection. NEW J CHEM 2018. [DOI: 10.1039/c8nj03242d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A label-free ratiometric fluorescent biosensor for detection of exonuclease was proposed through utilizing two individual DNA conformation-specific dyes (DAPI and NMM).
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Affiliation(s)
- Wei Hu
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
| | - Hengzhi Zhao
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
| | - Jing Jing
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
| | - Xiaoling Zhang
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
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9
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Li Z, Zhang Q, Huang H, Ren C, Ouyang S, Zhao Q. L-noradrenaline functionalized near-infrared fluorescence CdSeTe probe for the determination of urea and bioimaging of HepG2 Cells. Talanta 2017; 171:16-24. [DOI: 10.1016/j.talanta.2017.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/28/2022]
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10
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Ge J, Dong ZZ, Bai DM, Zhang L, Hu YL, Ji DY, Li ZH. A novel label-free fluorescent molecular beacon for the detection of 3′–5′ exonuclease enzymatic activity using DNA-templated copper nanoclusters. NEW J CHEM 2017. [DOI: 10.1039/c7nj01761h] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A label-free biosensor was developed for highly sensitive and selective determination of Exo III based on poly(T) molecular beacon-templated CuNPs.
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Affiliation(s)
- Jia Ge
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Zhen-Zhen Dong
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Dong-Mei Bai
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Lin Zhang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Ya-Lei Hu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Dan-Yang Ji
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Zhao-Hui Li
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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11
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Park KS, Lee CY, Kang KS, Park HG. Aptamer-mediated universal enzyme assay based on target-triggered DNA polymerase activity. Biosens Bioelectron 2016; 88:48-54. [PMID: 27499380 DOI: 10.1016/j.bios.2016.07.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 11/18/2022]
Abstract
We herein describe an innovative method for a universal fluorescence turn-on enzyme assay, which relies on the target enzyme-triggered DNA polymerase activity. In the first target recognition step, the target enzyme is designed to destabilize detection probe derived from an aptamer specific to DNA polymerase containing the overhang sequence and the complementary blocker DNA, which consequently leads to the recovery of DNA polymerase activity inhibited by the detection probe. This target-triggered polymerase activity is monitored in the second signal transduction step based on primer extension reaction coupled with TaqMan probe. Utilizing this design principle, we have successfully detected the activities of two model enzymes, exonuclease I and uracil DNA glycosylase with high sensitivity and selectivity. Since this strategy is composed of separated target recognition and signal transduction modules, it could be universally employed for the sensitive determination of numerous different target enzymes by simply redesigning the overhang sequence of detection probe, while keeping TaqMan probe-based signal transduction module as a universal signaling tool.
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Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea; Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea
| | - Kyoung Suk Kang
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea.
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12
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Xu M, Li B. Label-free fluorescence strategy for sensitive detection of exonuclease activity using SYBR Green I as probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:22-26. [PMID: 26117197 DOI: 10.1016/j.saa.2015.06.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 06/08/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
A label-free and sensitive fluorescence assay for exonuclease activity is developed using commercially available SYBR Green I (SG) dye as signal probe. A proof-of-concept of this assay has been demonstrated by using exonuclease III (Exo III) as a model enzyme. In this assay, double-stranded DNA (dsDNA) can bind SG, resulting in a strong fluorescence signal of SG. Upon the addition of Exo III, dsDNA would be digested, and SG emits very weak fluorescence. Thus, Exo III activity can be facilely measured with a simple fluorescence reader. This method has a linear detection range from 1 U/mL to 200 U/mL with a detection limit of 0.7 U/mL. This label-free approach is selective, simple, convenient and cost-efficient without any complex DNA sequence design or fluorescence dye label. The method not only provides a platform for monitoring activity and inhibition of exonuclease but also shows great potential in biological process researches, drug discovery, and clinic diagnostics.
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Affiliation(s)
- Min Xu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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13
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Lin Z, Liu Z, Zhang H, Su X. Near-infrared fluorescence probe for the determination of acid phosphatase and imaging of prostate cancer cells. Analyst 2015; 140:1629-36. [PMID: 25632410 DOI: 10.1039/c4an01868k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we developed a near-infrared mercaptopropionic acid (MPA)-capped CuInS2 quantum dot (QD) fluorescence probe for the detection of acid phosphatases (ACP), which is an important biomarker and indicator of prostate cancer. The fluorescence of CuInS2 QDs could be quenched by Cu(2+), and then the addition of adenosine-5'-triphosphate (ATP) could effectively turn on the quenched fluorescence due to the strong interaction between Cu(2+) and ATP. The ACP could catalyze the hydrolysis of ATP, which would disassemble the complex of Cu(2+)-ATP. Therefore, the recovered fluorescence could be quenched again by the addition of ACP. In our method, the limit of detection (LOD) is considerably low for ACP detection in solution. Using the CuInS2 QDs fluorescence probe, we successfully performed in vitro imaging of human prostate cancer cells.
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Affiliation(s)
- Zihan Lin
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
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14
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Zhang H, Lin Z, Su X. Label-free detection of exonuclease III by using dsDNA–templated copper nanoparticles as fluorescent probe. Talanta 2015; 131:59-63. [DOI: 10.1016/j.talanta.2014.07.065] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 11/26/2022]
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15
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Xu Q, Zhang Y, Zhang CY. A triple-color fluorescent probe for multiple nuclease assays. Chem Commun (Camb) 2015; 51:9121-4. [DOI: 10.1039/c5cc02177d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We develop a triple-color fluorescent probe which may function as a lab-on-a-DNA-molecule for simultaneous detection of multiple nucleases.
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Affiliation(s)
- Qinfeng Xu
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Yihong Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
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