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Hybridization-initiated exonuclease resistance strategy for simultaneous detection of multiple microRNAs. Talanta 2018; 190:248-254. [DOI: 10.1016/j.talanta.2018.07.070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/16/2018] [Accepted: 07/22/2018] [Indexed: 01/15/2023]
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2
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Zhang J, Sun Y, Lu J. A novel bioluminescent detection of exonuclease I activity based on terminal deoxynucleotidyl transferase-mediated pyrophosphate release. LUMINESCENCE 2018; 33:1157-1163. [PMID: 30047621 DOI: 10.1002/bio.3530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/04/2018] [Accepted: 06/09/2018] [Indexed: 01/13/2023]
Abstract
Here we report a novel bioluminescence (BL) method for exonuclease I (Exo I) detection based on terminal deoxynucleotidyl transferase (TdT)-mediated pyrophosphate release. An inert hairpin probe with a blocked protruding 3'-terminal biotinylated nucleotide was designed, and a blocked 3'-terminal nucleotide of the probe would be removed only in the presence of Exo I, thus rendering the probe with a free 3'-hydroxyl group. Subsequently, with nucleotide incorporation by TdT, huge amounts of pyrophosphates were generated. After the conversion of pyrophosphate to adenosine triphosphate (ATP) through ATP sulfurylase, BL was emitted by the reaction of d-luciferin and ATP with firefly luciferase. Therefore, Exo I activity was indirectly quantified in the range 1-500 mU with a detection limit of 0.05 mU/μl. Moreover, the developed approach was successfully applied to investigate the inhibitory effect of streptavidin on cleavage of Exo I and also determine Exo I activity in spiked serum samples. Overall, the proposed method has high sensitivity and selectivity, and can be universally extended to the detection of other nucleases using terminal extension as a signal amplification method and BL as a detection signal, having potential application in the diagnosis of nuclease-related diseases or evaluation of nuclease functions in biological systems.
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Affiliation(s)
- Jingjing Zhang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, China
| | - Yue Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, China
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Zhao J, Li C, Ma G, Hao W, Jia H. Colorimetric detection of protein via the terminal protection of small-molecule-linked DNA and unmodified gold nanoparticles. RSC Adv 2018; 8:38758-38764. [PMID: 35558333 PMCID: PMC9090659 DOI: 10.1039/c8ra07314g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 10/31/2018] [Indexed: 11/21/2022] Open
Abstract
A novel colorimetric strategy for protein detection was developed based on unmodified gold nanoparticles (AuNPs) and terminal protection from a target protein.
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Affiliation(s)
- Jianwei Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
| | - Cuiping Li
- College of Public Health
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Hebei University
- Baoding
- P. R. China
| | - Guimin Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
| | - Wenhui Hao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
| | - Hongxia Jia
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
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4
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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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Gao X, Geng M, Li Y, Wang X, Yu HZ. Revealing and Resolving the Restrained Enzymatic Cleavage of DNA Self-Assembled Monolayers on Gold: Electrochemical Quantitation and ESI-MS Confirmation. Anal Chem 2017; 89:2464-2471. [PMID: 28192924 DOI: 10.1021/acs.analchem.6b04573] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we report a combined electrochemical and ESI-MS study of the enzymatic hydrolysis efficiency of DNA self-assembled monolayers (SAMs) on gold, platform systems for understanding nucleic acid surface chemistry, and for constructing DNA-based biosensors. Our electrochemical approach is based on the comparison of the amounts of surface-tethered DNA nucleotides before and after exonuclease I (Exo I) incubation using electrostatically bound [Ru(NH3)6]3+ as redox indicators. It is surprising to reveal that the hydrolysis efficiency of ssDNA SAMs does not depend on the packing density and base sequence, and that the cleavage ends with surface-bound shorter strands (9-13 mers). The ex-situ ESI-MS observations confirmed that the hydrolysis products for ssDNA SAMs (from 24 to 56 mers) are dominated with 10-15 mer fragments, in contrast to the complete digestion in solution. Such surface-restrained hydrolysis behavior is due to the steric hindrance of the underneath electrode to the Exo I/DNA binding, which is essential for the occurrence of Exo I-catalyzed processive cleavage. More importantly, we have shown that the hydrolysis efficiency of ssDNA SAMs can be remarkably improved by adopting long alkyl linkers (locating DNA strands further away from the substrates).
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Affiliation(s)
- Xiaoyi Gao
- Department of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Mingxi Geng
- Department of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Yunchao Li
- Department of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Xinglin Wang
- Department of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Hua-Zhong Yu
- Department of Chemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
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Shi H, Mao X, Chen X, Wang Z, Wang K, Zhu X. The analysis of proteins and small molecules based on sterically tunable nucleic acid hyperbranched rolling circle amplification. Biosens Bioelectron 2016; 91:136-142. [PMID: 28006680 DOI: 10.1016/j.bios.2016.12.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/15/2022]
Abstract
In this work, we succeeded in establishing a new method for proteins and small molecules analysis based on the small molecule-linked DNA and nucleic acid hyperbranched rolling circle amplification (HRCA). Small molecule linked DNA by chemical modification was used as a flexible tool to study protein-small molecule interactions. The HRCA reaction which would produce signal amplification was regulated by the steric effect depending on whether the target proteins were present. In the implement of the proposed strategy, streptavidin (SA)-biotin and anti-digoxin antibody (anti-Dig)-digoxin were chosen as two model partners. Experimental results showed that the quantitative detection of SA and anti-Dig was realized both with nanomolar detection limits. The small molecules biotin and digoxin were also detected at nanomolar levels in a wide range of 1nM~100µM and 1nM~10µM, respectively. Meanwhile, the results indicated that the method had a favorable specificity in analyzing proteins or small molecules. Thus, it may be expected to quantitatively analyze some protein markers and small molecular drugs in complex biological samples.
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Affiliation(s)
- Hai Shi
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaoxia Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Zihan Wang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Keming Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China.
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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Ban F, Shi H, Feng C, Mao X, Yin Y, Zhu X. A one-pot strategy for the detection of proteins based on sterically and allosterically tunable hybridization chain reaction. Biosens Bioelectron 2016; 86:219-224. [PMID: 27376192 DOI: 10.1016/j.bios.2016.06.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 01/05/2023]
Abstract
In this work, we report a facile one-pot strategy for protein detection based on sterically and allosterically tunable hybridization chain reaction (HCR). In our strategy, DNA hairpins H1 and H2 are dual-labeled with pyrene moieties through a six-carbon-atom spacer at each end; and a single-stranded DNA primer is designed to contain two small molecules near each end. In the absence of target protein, the primer can trigger HCR events between alternating H1 and H2 hairpins to form a nicked double-helix. As a result, the pyrene excimers are formed to emit at approximately 485nm. On the contrary, upon binding of the specific target protein onto the primer through the protein-small molecule interaction, the HCR will be inhibited due to the steric and allosteric effect. The changes of the fluorescent signals of pyrene excimers are in response to the concentration of target protein, so that the detection of protein can be realized. We have demonstrated the feasibility of this strategy by using streptavidin (SA) and folate receptor (FR) as model targets. Results show that both of them can be well detected with a detection limit of 1.07nM and 2.7nM, respectively. The developed method for protein assay is flexible, so we infer that the one-pot strategy holds great potential for the detection of other proteins.
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Affiliation(s)
- Fangfang Ban
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Hai Shi
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, Nanjing University, Nanjing 210093, China
| | - Chang Feng
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, Nanjing University, Nanjing 210093, China
| | - Xiaoxia Mao
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yongmei Yin
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Xiaoli Zhu
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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