1
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Tang NC, Su JC, Shmidov Y, Kelly G, Deshpande S, Sirohi P, Peterson N, Chilkoti A. Synthetic intrinsically disordered protein fusion tags that enhance protein solubility. Nat Commun 2024; 15:3727. [PMID: 38697982 PMCID: PMC11066018 DOI: 10.1038/s41467-024-47519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
We report the de novo design of small (<20 kDa) and highly soluble synthetic intrinsically disordered proteins (SynIDPs) that confer solubility to a fusion partner with minimal effect on the activity of the fused protein. To identify highly soluble SynIDPs, we create a pooled gene-library utilizing a one-pot gene synthesis technology to create a large library of repetitive genes that encode SynIDPs. We identify three small (<20 kDa) and highly soluble SynIDPs from this gene library that lack secondary structure and have high solvation. Recombinant fusion of these SynIDPs to three known inclusion body forming proteins rescue their soluble expression and do not impede the activity of the fusion partner, thereby eliminating the need for removal of the SynIDP tag. These findings highlight the utility of SynIDPs as solubility tags, as they promote the soluble expression of proteins in E. coli and are small, unstructured proteins that minimally interfere with the biological activity of the fused protein.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jonathan C Su
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Parul Sirohi
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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2
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Wu Q, Yu Y, Chen M, Long J, Yang X. A label-free fluorescence sensing strategy based on GlaI-assisted EXPAR for rapid and accurate quantification of human methyltranferase activity. Talanta 2024; 269:125456. [PMID: 38061202 DOI: 10.1016/j.talanta.2023.125456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/23/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
DNA methylation plays an important role in epigenetic modification. DNA methyltransferase (DNMT) is essential in the DNA methylation process, and its abnormal expression is closely related to cancer. In this study, we propose a novel biosensor platform (DS-GlaI-EXPAR) that combines hemi-methylated double-stranded DNA (dsDNA) as the substrate for DNMT1 with GlaI-assisted isothermal exponential amplification reaction (EXPAR) for rapid, simple, and sensitive detection of DNMT1 activity. The hemi-methylated dsDNA is fully methylated by DNMT1, and GlaI recognizes and cleaves the fully methylated sequence, generating terminal fragments that trigger EXPAR for efficient signal amplification. Whereas hemi-methylated dsDNA without DNMT1 will keep intact and cannot initiate EXPAR. DNMT1 activity can therefore be sensitively quantified by the real-time fluorescence signal of the DS-GlaI-EXPAR platform. The high-efficiency amplification of EXPAR and the recognition of GlaI enable the platform to overcome the inherent cumbersome and time-consuming shortcomings of traditional methods while meeting specificity and sensitivity. This DS-GlaI-EXPAR platform offers an impressively low limit of detection of 0.86 pg/μL and the entire detection process can be completed in a short time of 2.5 h in a single tube. Furthermore, DNMT1 activity detected by this platform in MCF-7 cells was significantly higher than that of HEK293 cells, and the inhibition of Apt. #9 was verified. This DNMT1 activity detection platform is very convenient and effective for the discovery of inhibitors and early cancer diagnosis.
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Affiliation(s)
- Qiaomin Wu
- Clinical Laboratory, Dongyang People's Hospital, Dongyang, Zhejiang, 322100, China; Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Chen CA, Ho NYJ, Hsiao HY, Lin SS, Lai PL, Tsai TT. Smartphone-assisted fluorescence-based detection of sunrise-type smart amplification process and a 3D-printed ultraviolet light-emitting diode device for the diagnosis of tuberculosis. Biosens Bioelectron 2024; 244:115799. [PMID: 37918047 DOI: 10.1016/j.bios.2023.115799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Accurate and rapid diagnosis of infectious diseases plays a key role in clinical practice, especially in resource-limited countries. In this study, we integrated sunrise-type smart amplification process (s-SmartAmp), a convenient and sensitive isothermal amplification method for nucleic acid, into a portable 3D-printed device equipped with smartphone-assisted image analysis capabilities to develop a novel fluorescence-based sensing system for the on-site diagnosis of tuberculosis (TB). To increase the efficiency of fluorescence (or Förster) resonance energy transfer, two types of sunrise probe systems were compared to detect the IS6110 DNA sequence of TB. Subsequently, linear regression was conducted to compare the performance of s-SmartAmp and loop-mediated isothermal amplification (LAMP). The results indicated that, compared with LAMP, s-SmartAmp yielded more stable and precise results with lower background interference and high linear correlation coefficients (R2 = 0.9994 and 1, respectively) for the FAM-TAMRA and FITC-BHQ-1 probe system. The detection time was 45 min with a detection limit of 10 fg/μL. To evaluate the performance of our proposed on-site sensing system, we used s-SmartAmp 3D-printed ultraviolet light-emitting diode device to test multiple clinical samples of TB. Our findings suggest that the proposed system has the potential to achieve accurate and rapid on-site diagnosis of TB.
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Affiliation(s)
- Chung-An Chen
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hui-Yi Hsiao
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Song-Shu Lin
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Po-Liang Lai
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University, Taoyuan, Taiwan.
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4
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Yang H, Zhu L, Wang X, Song Y, Dong Y, Xu W. Extension characteristics of TdT and its application in biosensors. Crit Rev Biotechnol 2023:1-15. [PMID: 37880088 DOI: 10.1080/07388551.2023.2270772] [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: 05/30/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023]
Abstract
The advantages of rapid amplification of nucleic acid without a template based on terminal deoxyribonucleotidyl transferase (TdT) have been widely used in the field of biosensors. However, the catalytic efficiency of TdT is affected by extension conditions. The sensitivity of TdT- mediated biosensors can be improved only under appropriate conditions. Therefore, in this review, we provide a comprehensive overview of TdT extension characteristics and its applications in biosensors. We focus on the relationship between TdT extension conditions and extension efficiency. Furthermore, the construction strategy of TdT-mediated biosensors according to five different recognition types and their applications in targets are discussed and, finally, several current challenges and prospects in the field are taken into consideration.
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Affiliation(s)
- He Yang
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Longjiao Zhu
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Xinxin Wang
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Yuhan Song
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Food Science and Nutritional Engineering, Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), China Agricultural University, Beijing, China
| | - Yulan Dong
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wentao Xu
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Food Science and Nutritional Engineering, Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), China Agricultural University, Beijing, China
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5
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Yi M, Gong Y, Zhan Q, Dai Y, Yang T, Cheng X, Ding S, Gu B, Cheng W, Zhang D. A one-pot CRISPR-Cas12a-based toolbox enables determination of terminal deoxynucleotidyl transferase activity for acute leukemia screening. Anal Chim Acta 2023; 1254:341115. [PMID: 37005025 DOI: 10.1016/j.aca.2023.341115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
An isothermal, one-pot toolbox (called OPT-Cas) based on CRISPR-Cas12a collateral cleavage capability is proposed for highly sensitive and selective determination of terminal deoxynucleotidyl transferase (TdT) activity. Oligonucleotide primers with 3'-hydroxyl (OH) terminal were randomly introduced for TdT-induced elongation. In the presence of TdT, dTTP nucleotides polymerized at the 3' terminals of the primers to generate abundant polyT-tails, which function as triggers for the synchronous activation of Cas12a proteins. Finally, the activated Cas12a trans-cleaved FAM and BHQ1 dual-labeled single-stranded DNA (ssDNA-FQ) reporters, producing significantly amplified fluorescence signals. This one-pot assay, that is primer, crRNA, Cas12a protein and ssDNA-FQ reporter are all in one tube, allows simple but high-sensitive quantification of TdT activity with a low detection limit of 6.16 × 10-5 U μL-1 in the concentration scope from 1 × 10-4 U μL-1 to 1 × 10-1 U μL-1, and achieves extraordinary selectivity with other interfering proteins. Furthermore, the OPT-Cas was successfully used to detect TdT in complex matrices and accurate determination of TdT activity in acute lymphoblastic leukemia cells, which might be a reliable technique platform for the diagnosis of TdT-related diseases and biomedical research applications.
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6
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Colorimetric aptasensor based on spherical nucleic acid-induced hybridization chain reaction for sensitive detection of exosomes. Talanta 2023; 258:124453. [PMID: 36924637 DOI: 10.1016/j.talanta.2023.124453] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/02/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023]
Abstract
Exosomes are one of the most promising biomarkers for tumor diagnosis and prognosis. Therefore, the development of convenient and sensitive exosome sensing strategies is of great significance. Herein, we integrated aptamer-based spherical nucleic acids (SNAs) and hybridization chain reaction (HCR) into a colorimetric aptasensor platform and applied it to the detection of exosomes. In this design, the CD63-specific aptamer pre-immobilized on the microplate was used to capture target exosomes, while the SNAs conjugated with nucleolin-specific aptamer and trigger probe H1 were designed for amplifying signal. In the presence of target exosomes, the SNAs can be attached to the microplate by the bridge effect of exosomes, resulting in the trigger of HCR. This process is accompanied by the formation of abundant G-quadruplex/hemin DNAzyme, enabling the visual quantitative analysis of exosomes. Featured with the dual amplification of SNAs and HCR, the proposed aptasensor achieved a considerable detection limit of 50 particles/μL. The practicability of this method was further verified by testing the different clinical samples. Given the ability of the aptasensor to visually detect exosomes in scenarios lacking instruments and resources, we believe that the aptasensor can be serve as a potential on-site test for liquid biopsy.
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7
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Ye W, Zhang Z, Wang C, Feng Z, Hu Z, Liu Q, Wu T. Detection of small molecules by extending the terminal protection to the polymerase. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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8
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Ashley J, Potts IG, Olorunniji FJ. Applications of Terminal Deoxynucleotidyl Transferase Enzyme in Biotechnology. Chembiochem 2023; 24:e202200510. [PMID: 36342345 DOI: 10.1002/cbic.202200510] [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: 09/01/2022] [Revised: 11/04/2022] [Indexed: 11/09/2022]
Abstract
The use of polymerase enzymes in biotechnology has allowed us to gain unprecedented control over the manipulation of DNA, opening up new and exciting applications in areas such as biosensing, polynucleotide synthesis, and DNA storage, aptamer development and DNA-nanotechnology. One of the most intriguing enzymes which has gained prominence in the last decade is terminal deoxynucleotidyl transferase (TdT), which is one of the only polymerase enzymes capable of catalysing the template independent stepwise addition of nucleotides onto an oligonucleotide chain. This unique enzyme has seen a significant increase in a variety of different applications. In this review, we give a comprehensive discussion of the unique properties and applications of TdT as a biotechnology tool, and the application in the enzymatic synthesis of poly/oligonucleotides. Finally, we look at the increasing role of TdT enzyme in biosensing, DNA storage, synthesis of DNA nanostructures and aptamer development, and give a future outlook for this technology.
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Affiliation(s)
- Jon Ashley
- School of Pharmaceutical and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, 3 Byrom St, Liverpool, L3 3AF, UK
| | - Indiia G Potts
- School of Pharmaceutical and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, 3 Byrom St, Liverpool, L3 3AF, UK
| | - Femi J Olorunniji
- School of Pharmaceutical and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, 3 Byrom St, Liverpool, L3 3AF, UK
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9
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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10
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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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Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria. Front Microbiol 2023; 14:1129437. [PMID: 37032876 PMCID: PMC10073500 DOI: 10.3389/fmicb.2023.1129437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuwei Wang
- Key Laboratory of Livestock and Poultry Provenance Disease Research in Mianyang, Sichuan, China
| | - Longgui He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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12
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A sensing strategy combining T7 promoter-contained DNA probe with CRISPR/Cas13a for detection of bacteria and human methyltransferase. Anal Chim Acta 2022; 1227:340266. [DOI: 10.1016/j.aca.2022.340266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]
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13
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Kim TY, Lim MC, Lim JA, Choi SW, Woo MA. Microarray detection method for pathogen genes by on-chip signal amplification using terminal deoxynucleotidyl transferase. MICRO AND NANO SYSTEMS LETTERS 2022. [DOI: 10.1186/s40486-022-00153-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractA microarray detection method based on on-chip signal amplification using terminal deoxynucleotidyl transferase (TdT) was developed to visualize pathogenic genes. Cyclic olefin copolymer (COC) substrate for microarrays was treated with oxygen plasma to induce hydrophilic surface properties. The capture probe DNA was immobilized on the COC surface by UV irradiation. The 3ʹ end of the capture probe DNA immobilized on the COC surface was modified with a phosphate group to provide resistance against the TdT reaction. Therefore, the TdT reaction was triggered only when the capture probe DNA acquired the target gene, and biotin-11-deoxyuridine triphosphate (b-dUTP) was continuously added to the 3ʹ end of the target gene. Thereafter, streptavidin-conjugated gold nanoparticles (s-AuNPs) tagged the poly uridine tails by the biotin–streptavidin interaction. The visual signal was amplified by silver enhancement in the presence of the s-AuNPs. The usefulness of this detection method was confirmed by analyzing four pathogens and allowing their visual identification.
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14
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Simple Detection of DNA Methyltransferase with an Integrated Padlock Probe. BIOSENSORS 2022; 12:bios12080569. [PMID: 35892466 PMCID: PMC9332213 DOI: 10.3390/bios12080569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022]
Abstract
DNA methyltransferases (MTases) can be regarded as biomarkers, as demonstrated by many studies on genetic diseases. Many researchers have developed biosensors to detect the activity of DNA MTases, and nucleic acid amplification, which need other probe assistance, is often used to improve the sensitivity of DNA MTases. However, there is no integrated probe that incorporates substrates and template and primer for detecting DNA MTases activity. Herein, we first designed a padlock probe (PP) to detect DNA MTases, which combines target detection with rolling circle amplification (RCA) without purification or other probe assistance. As the substrate of MTase, the PP was methylated and defended against HpaII, lambda exonuclease, and ExoI cleavage, as well as digestion, by adding MTase and the undestroyed PP started RCA. Thus, the fluorescent signal was capable of being rapidly detected after adding SYBRTM Gold to the RCA products. This method has a detection limit of approximately 0.0404 U/mL, and the linear range was 0.5–110 U/mL for M.SssI. Moreover, complex biological environment assays present prospects for possible application in intricacy environments. In addition, the designed detection system can also screen drugs or inhibitors for MTases.
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15
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Lu X, Li D, Luo Z, Duan Y. A dual-functional fluorescent biosensor based on enzyme-involved catalytic hairpin assembly for the detection of APE1 and miRNA-21. Analyst 2022; 147:2834-2842. [PMID: 35621039 DOI: 10.1039/d2an00108j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Both apurinic/apyrimidinic endonuclease 1 (APE1) and microRNA-21 (miRNA-21) have been reported to be related to tumors, enabling them to be the biomarkers of several cancers. This has led to the development of various biosensors to detect APE1 or miRNA-21. However, biosensors that focus on single target detection are subject to low accuracy. In this work, a fluorescent biosensor based on enzyme-involved catalytic hairpin assembly (CHA) for the detection of APE1 and miRNA-21 was developed, aimed at improving the accuracy of early-phase diagnosis of cancers. Two hairpin structured DNA probes (H1 and H2) were utilized to concatenate the enzyme-assisted circuit and CHA circuit in the system. The stem of H1 with a blunt end was modified with an AP site, while H2 was modified with 6-FAM at the 5' terminal and Dabcyl at the 3' terminal. In the presence of APE1, H1 was cleaved from the AP site to expose the toehold sequence. Then, miRNA-21 bound with the toehold sequence to initiate the CHA reaction between H1 and H2. The assembled product of CHA triggered the 6-FAM of H2 at a distance from Dabcyl, which recovered the fluorescence signal. It is worth noting that only under the co-stimulation of APE1 and miRNA-21 can the fluorescence signal be detected, indicating that the biosensor could work as an AND logic gate. The proposed dual-functional biosensor achieved a limit of detection (LOD) of 0.016 U mL-1 for APE1 and 0.25 nM for miRNA-21 and APE1, respectively, and also exhibits good selectivity and stability for the two biomarkers. Thus, the biosensor has great potential to be applied as a new platform for cancer diagnosis.
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Affiliation(s)
- Xiaoyong Lu
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P.R. China.
| | - Dan Li
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, Shaanxi, P.R. China.
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, Shaanxi, P.R. China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P.R. China.
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16
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Huang C, Shen G, Ding S, Kan A, Jiang D, Jiang W. Primer-template conversion-based cascade signal amplification strategy for sensitive and accurate detection of polynucleotide kinase activity. Anal Chim Acta 2021; 1187:339139. [PMID: 34753572 DOI: 10.1016/j.aca.2021.339139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/25/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022]
Abstract
Here, a primer-template conversion-based cascade signal amplification strategy is described for the sensitive detection of polynucleotide kinase (PNK) activity. This strategy integrated rolling circle amplification (RCA) and multiple-repeated-strand displacement amplification (MRSDA) with G-quadruplex based fluorescence lighting-up assay. A delicate dumbbell-shaped DNA probe with 5'-hydroxyl terminus was designed, in which G-quadruplex and half recognition site of nicking enzyme Nb.BbvCI were encoded in two loops respectively. Under the action of PNK, the 5' terminus on dumbbell probe was firstly phosphorylated, and then the dumbbell was cyclized with the catalyzation of T4 ligase to become the RCA template. The RCA process produced multiple copies of the prolonged primer. After that, under the assistance of nicking enzyme Nb.BbvCI, a primer-template conversion occurred, which converted the primer and template of RCA into the template and primer of the subsequent MRSDA, respectively. The MRSDA generated multiple repeated ssDNA sequences which possessed G-quadruplexes for outputting signal by lighting-up fluorescence of thioflavin T (ThT). The cascade signal amplification of RCA and MRSDA provided high detection sensitivity, and the target-dependence of template in cascade signal amplification led to a low background. The method showed excellent detection limit of 0.2 × 10-6 U μL-1 in buffer and 5 cells in cell lysate sample. Moreover, this method displayed favorable selectivity when interfering proteins were present. The developed strategy has good practical potential for PNK activity detection in clinical diagnosis and medical research.
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Affiliation(s)
- Chao Huang
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Guohong Shen
- Breast Center, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, 250013, Jinan, PR China
| | - Shengyong Ding
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Ailing Kan
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Dafeng Jiang
- Department of Physical and Chemical Testing, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, 250014, Jinan, PR China.
| | - Wei Jiang
- Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China; School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
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17
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Zhang Y, Han Y, Zou X, Xu Q, Ma F, Zhang CY. Construction of a damage site-specific fluorescent biosensor for single-molecule detection of DNA damage. Talanta 2021; 235:122809. [PMID: 34517666 DOI: 10.1016/j.talanta.2021.122809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 02/06/2023]
Abstract
The 8-oxoguanine (8-oxoG) represents the most common DNA damage type, and it has been regarded as the oxidative stress biomarker, but the reported 8-oxoguanine assays are limited by poor specificity and low sensitivity. Herein, we demonstrate the construction of damage site-specific fluorescent biosensor for 8-oxoG assay by integrating single-molecule detection with hyperbranched signal amplification. In this assay, the 8-oxoG damages in DNA can generate free 3' OH with the assistance of formamidopyrimidine DNA glycosylase (Fpg) and polynucleotide kinase (PNK), which subsequently triggers the incorporation of abundant Cy5-labeled dUTPs via terminal deoxynucleotidyl transferase (TDT)-mediated site-specific hyperbranched nucleic acid amplification. After digestion of amplification products with nuclease treatment, abundant mononucleotide Cy5-dUTPs are produced, which will be easily monitored via single-molecule imaging and detection. The introduction of hyperbranched nucleic acid amplification and single-molecule detection can greatly improve the sensitivity to achieve a detection limit of 7.62 × 10-18 M. This biosensor is highly specific with the capability of discriminating 0.001% 8-oxoG target from the DNA mixture. Moreover, it can be applied for quantitative detection of 8-oxoG damage in genomic DNAs with a detection limit of 0.0017 ng, and even accurately quantifies the absolute number (7025 - 8506) of 8-oxoG damage base in single HeLa cell treated with 150 μM H2O2. Importantly, this biosensor can measure the 8-oxoG damage level in different cancer cell lines, facilitating the oxidative damage-associated biomedical researches and clinical diagnosis.
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Affiliation(s)
- Yan 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
| | - Yun Han
- 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
| | - Xiaoran Zou
- 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
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, 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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18
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Ye W, Li L, Feng Z, Tu B, Hu Z, Xiao X, Wu T. Sensitive detection of alkaline phosphatase based on terminal deoxynucleotidyl transferase and endonuclease IV-assisted exponential signal amplification. J Pharm Anal 2021; 12:692-697. [PMID: 36105169 PMCID: PMC9463482 DOI: 10.1016/j.jpha.2021.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/31/2021] [Accepted: 09/17/2021] [Indexed: 12/27/2022] Open
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19
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Zhang YP, Wang HP, Dong RL, Li SY, Wang ZG, Liu SL, Pang DW. Proximity-induced exponential amplification reaction triggered by proteins and small molecules. Chem Commun (Camb) 2021; 57:4714-4717. [PMID: 33977980 DOI: 10.1039/d1cc00583a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We proposed a method to regulate nucleic acid polymerization by proximity and designed an ultrasensitive biosensor based on proximity-induced exponential amplification reaction for proximity assay of proteins (streptavidin) and small molecules (adenosine triphosphate), which allows us to detect a variety of interesting targets by simply changing the binding sites of DNA.
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Affiliation(s)
- Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China.
| | - Hong-Peng Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China.
| | - Ruo-Lan Dong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China.
| | - Si-Yao Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China.
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China.
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China. and Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China.
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20
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Huang W, Zhou Y, Zhan D, Lai G. Homogeneous biorecognition reaction-induced assembly of DNA nanostructures for ultrasensitive electrochemical detection of kanamycin antibiotic. Anal Chim Acta 2021; 1154:338317. [PMID: 33736811 DOI: 10.1016/j.aca.2021.338317] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/16/2023]
Abstract
By the employment of a homogeneous biorecognition reaction to induce the assembled formation of DNA nanostructures at an electrode, herein we develop a novel biosensing method for the ultrasensitive electrochemical detection of kanamycin (Kana) antibiotic. A DNA complex consisting of Kana-aptamer and a hairpin DNA with an exposed 3'-end was first designed for conducting the homogeneous reaction with Kana in the presence of exonuclease I (Exo I). It resulted in the production of a hairpin DNA with a blunt terminus, which could be used for triggering the assembled formation of a layer of DNA nanostructures with orderly distribution and abundant biotin sites at a gold electrode. Then, high-content methylene blue and horseradish peroxidase (HRP)-functionalized gold nanotags would be captured onto the electrode to realize the electrocatalytic signal transduction. Due to the Exo I and HRP-assisted dual signal amplification, a very low detection limit of 9.1 fg mL-1 was obtained for the Kana assay along with a very wide linear range over five-order of magnitude. Considering the excellent performance of the method, it exhibits a promising prospect for practical applications.
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Affiliation(s)
- Wan Huang
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, China
| | - Yue Zhou
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, China
| | - Danyan Zhan
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, China
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, China.
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21
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Terminal deoxynucleotidyl transferase combined CRISPR-Cas12a amplification strategy for ultrasensitive detection of uracil-DNA glycosylase with zero background. Biosens Bioelectron 2021; 171:112734. [DOI: 10.1016/j.bios.2020.112734] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 12/26/2022]
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22
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Cui W, Hu G, Song F, Wang R, Cao Z, Zhang J, Wang T, Meng F, Shen C, Xu S, Wang J. A cascade strand displacement amplification strategy for highly sensitive and label-free detection of DNA methyltransferase activity. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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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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24
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Zhang S, Su X, Wang J, Chen M, Li C, Li T, Ge S, Xia N. Nucleic Acid Testing for Coronavirus Disease 2019: Demand, Research Progression, and Perspective. Crit Rev Anal Chem 2020; 52:413-424. [PMID: 32813575 DOI: 10.1080/10408347.2020.1805294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a public health emergency of international concern. There has been a surge in demand for COVID-19 diagnostic reagents, as timely detection of virus carriers is one of the most important components of disease prevention and control. Nucleic acid testing (NAT), with high sensitivity and specificity, is considered the "gold standard" for the diagnosis of COVID-19. Therefore, more than 700 research units and companies have been devoted to developing NAT reagents. To date, nearly 600 research units and companies have claimed to have completed the development of NAT reagents. The use of these products has a positive effect on disease prevention and control; however, exaggerated claims and inadequate understanding of the products have led to improper access to reagents and equipment in clinics. This has resulted in chaos in the clinical diagnosis of COVID-19. Herein, we have overviewed the COVID-19 NAT products, including their principles, corresponding advantages and disadvantages, relevant circumstances for application, and respective roles in epidemic containment. Our comments may provide some references for assay developers and aid clinical staff in choosing the appropriate class of test from the different tests available.
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Affiliation(s)
- Shiyin Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Xiaosong Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Jin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China.,School of Life Sciences, Xiamen University, Xiamen, China
| | - Mengyuan Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Caiyu Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China.,School of Life Sciences, Xiamen University, Xiamen, China
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25
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A molecular device: A DNA molecular lock driven by the nicking enzymes. Comput Struct Biotechnol J 2020; 18:2107-2116. [PMID: 32913580 PMCID: PMC7451616 DOI: 10.1016/j.csbj.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.
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26
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Zhang Y, Hao L, Zhao Z, Yang X, Wang L, Liu S. Immuno-DNA binding directed template-free DNA extension and enzyme catalysis for sensitive electrochemical DNA methyltransferase activity assay and inhibitor screening. Analyst 2020; 145:3064-3072. [DOI: 10.1039/d0an00008f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new electrochemical immuno-DNA sensing platform for DNA methyltransferase activity assay and inhibitor screening.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Lijie Hao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Zhen Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xiaoyan Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Li Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Shufeng Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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