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Li B, Jiang H, Luo S, Zeng Z, Xu X, Li X, Zhang S, Chen Y, Ding S, Li X, Liu J, Chen W. Enzyme-accelerated catalytic DNA circuits enable rapid and one-pot detection of bacterial pathogens. Biosens Bioelectron 2024; 267:116822. [PMID: 39362139 DOI: 10.1016/j.bios.2024.116822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/27/2024] [Accepted: 09/28/2024] [Indexed: 10/05/2024]
Abstract
Catalytic DNA circuits, serving as signal amplification strategies, can enable simple and accurate detection of pathogenic bacteria in complex matrices but suffer from low reaction rates and depths. Herein, we design an enzyme-accelerated catalytic hairpin assembly (EACHA) in which duplex DNA products are converted into hairpin reactants to continue participating in the next circuit reaction with the assistance of RNase H. Profiting from the high recyclability of the reactants, EACHA exhibits an approximately 37.6-fold enhancement in the rate constant and a two-order-of-magnitude improvement in sensitivity compared to conventional catalytic hairpin assembly (CHA). By integrating an allosteric probe with EACHA, a one-pot method is developed for rapid and direct detection of S. enterica Enteritidis (S. Enteritidis). This method is capable of detecting 15 CFU mL-1 of S. Enteritidis within 20 min, which is superior to that of real-time PCR. By testing 60 milk samples, we demonstrate this method's high accuracy in discriminating contaminated samples, with an area under the curve (AUC) of 0.997. Moreover, this method can be employed to accurately diagnose early-stage infected mice, with an AUC of 1.00 for feces samples and 0.986 for serum samples. Therefore, this study offers a simple and feasible method for identifying pathogens in complex matrices.
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Affiliation(s)
- Baolin Li
- School of Medicine, Xi'an Jiaotong University, 710061, Xi'an, PR China; Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, 646000, Luzhou, PR China
| | - Hui Jiang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, 646000, Luzhou, PR China
| | - Sijian Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, 646000, Luzhou, PR China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, 646000, Luzhou, PR China
| | - Xuejing Xu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, 646000, Luzhou, PR China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, PR China
| | - Songzhi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, PR China
| | - Yirong Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, PR China
| | - Xinmin Li
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, 400011, Chongqing, PR China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, 646000, Luzhou, PR China
| | - Wei Chen
- School of Medicine, Xi'an Jiaotong University, 710061, Xi'an, PR China; Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, PR China.
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Qi F, Li H, Wang Y, Ding C. Responsive DNA hydrogels: design strategies and prospects for biosensing. Chem Commun (Camb) 2024; 60:10231-10244. [PMID: 39171719 DOI: 10.1039/d4cc03829k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Hydrogels, water-filled networks that can adapt to external stimuli by altering their volume, are known for their high flexibility and biocompatibility. DNA, a critical biomolecule renowned for its exceptional characteristics including information transmission, molecular recognition, and editability, has found widespread applications in the biosensing field as well. The integration of these two biomaterials offers promising opportunities for the development of novel biosensors with enhanced sensitivity, specificity, and adaptability. Therefore, by virtue of the collective features, researchers have recently focused on the construction of responsive DNA hydrogel systems. This feature article describes recent developments in fabricating DNA hydrogels and their applications in the biosensing area. Initially, it focuses on the design strategies employed in preparing DNA hydrogels, encompassing both pure DNA hydrogels and hybridized DNA hydrogels. Subsequently, it summarizes the use of DNA hydrogels in biosensing applications, highlighting their applications in visual detection, electrochemical sensing, and optical biosensing analyses. Furthermore, the underlying responsive mechanisms within these biosensing systems are also described. Lastly, this article presents a comprehensive discussion on the existing challenges and prospects of responsive DNA hydrogels, offering insights into their potential to revolutionize the field of biosensing.
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Affiliation(s)
- Fenglian Qi
- 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, Shandong, 266042, P. R. China.
| | - Hanwen Li
- 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, Shandong, 266042, P. R. China.
| | - Yonghao 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, Shandong, 266042, P. R. China.
| | - Caifeng Ding
- 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, Shandong, 266042, P. R. China.
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Jiang H, Peng Z, Lv X, Liu Y, Li X, Deng Y. Hybrid chain reaction nanoscaffold-based functional nucleic acid nanomaterial cascaded with rolling circle amplification for signal enhanced miRNA let-7a detection. Mikrochim Acta 2024; 191:533. [PMID: 39134753 DOI: 10.1007/s00604-024-06617-5] [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: 05/02/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024]
Abstract
A novel functional nucleic acid (FNA) nanomaterial based on hybrid chain reaction (HCR) nanoscaffolds is proposed to solve the problem of time superposition and repeated primer design in sensitive miRND detection using cascade amplification technique. Rolling circle amplification (RCA) was cascaded with the prepared FNA nanomaterials for miRNA let-7a (as a model target) sensitive detection by lateral flow assay (LFA). Under the optimal conditions, the proposed RCA-FNA-LFA assay demonstrated the specificity and accuracy for miRNA let-7a detection with a detection limit of 1.07 pM, which increased sensitivity by nearly 20 times compared with that of RCA -LFA assay. It is worth noting that the non-target-dependent self-assembly process of HCR nanoscaffolds does not take up the whole detection time, thus, less time is taken than that of the conventional cascaded method. Moreover, the proposed assay does not need to consider the system compatibility between two kinds of isothermal amplification techniques. As for detection of different miRNAs, only the homologous arm of the padlock probe of RCA needs to be changed, while the FNA nanomaterial does not need any change, which greatly simplifies the primer design of the cascaded amplification techniques. With further development, the proposed RCA-FNA-LFA assay might achieve more sensitive and faster results to better satisfy the requirements of clinical diagnosis combing with more sensitive labels or small strip reader.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhao Peng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Ying Liu
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
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Liao Y, Yin X, Liu W, Du Z, Du J. Chaperone Copolymer-Assisted Catalytic Hairpin Assembly for Highly Sensitive Detection of Adenosine. Polymers (Basel) 2024; 16:2179. [PMID: 39125205 PMCID: PMC11314456 DOI: 10.3390/polym16152179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Adenosine is an endogenous molecule that plays a vital role in biological processes. Research indicates that abnormal adenosine levels are associated with a range of diseases. The development of sensors capable of detecting adenosine is pivotal for early diagnosis of disease. For example, elevated adenosine levels are closely associated with the onset and progression of cancer. In this study, we designed a novel DNA biosensor utilizing chaperone copolymer-assisted catalytic hairpin assembly for highly sensitive detection of adenosine. The functional probe comprises streptavidin magnetic beads, an aptamer, and a catalytic chain. In the presence of adenosine, it selectively binds to the aptamer, displacing the catalytic chain into the solution. The cyclic portion of H1 hybridizes with the catalytic strand, while H2 hybridizes with the exposed H1 fragment to form an H1/H2 complex containing a G-quadruplex. Thioflavin T binds specifically to the G-quadruplex, generating a fluorescent signal. As a nucleic acid chaperone, PLL-g-Dex expedites the strand exchange reaction, enhancing the efficiency of catalytic hairpin assembly, thus amplifying the signal and reducing detection time. The optimal detection conditions were determined to be a temperature of 25 °C and a reaction time of 10 min. Demonstrating remarkable sensitivity and selectivity, the sensor achieved a lowest limit of detection of 9.82 nM. Furthermore, it exhibited resilience to interference in complex environments such as serum, presenting an effective approach for rapid and sensitive adenosine detection.
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Affiliation(s)
| | | | | | | | - Jie Du
- School of Materials Science and Engineering, Hainan University, Haikou 570228, China; (Y.L.); (X.Y.); (W.L.); (Z.D.)
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Nie L, Zeng X, Li H, Wang S, Yu R. Enzyme-assisted amplification of target cycle triggers the unlocking of locked hairpin probes for let-7a detection. Talanta 2024; 266:125023. [PMID: 37549569 DOI: 10.1016/j.talanta.2023.125023] [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: 06/09/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
The detection of miRNA in cells is difficult owing to its substantially low cellular content. Therefore, developing a highly sensitive sensor to detect cellular miRNA remains a significant challenge. Herein, we report an enzyme-assisted biosensor with target cycle amplification that can trigger the unlocking of locked hairpin probes for sensitive and robust let-7a gene detection. In the research, three kinds of hairpin probes were skillfully designed. The hairpin probe comprises a complementary sequence of a target, primer, and recognition site of Nt. BbvCI restriction endonucleases. In addition, the alternating synergistic impact of polymerase and the nicking enzyme generates considerable triggers to unlock the locked hairpin probe LH1, consequently triggering a subsequent circulating strand displacement reaction to form a stable H1-H2 double strand to ensure sufficient distance between a fluorophore on H1 and a quenching group on bolt DNA (bDNA), and resulting in the recovery of fluorescence. Furthermore, this process does not require complicated operation procedures and instruments, and the target gene let-7a can be sensitively detected. Specifically, the detection limit of the biosensor is as low as 160 fM, and its linear range is 0.5 pM-250 nM. Moreover, this biosensor can be employed to detect let-7a in human serum with good selectivity.
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Affiliation(s)
- Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Xiaogang Zeng
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Hongbo Li
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
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Takemura S, Shimada N, Maruyama A. Malachite green-derivatized cationic comb-type copolymer acts as a photoresponsive artificial chaperone. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2023; 34:2463-2482. [PMID: 37787160 DOI: 10.1080/09205063.2023.2265127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
Molecular chaperones play vital roles in various physiological reactions by regulating the folding and assembly of biomacromolecules. We have demonstrated that cationic comb-type copolymers exhibit chaperone activity for anionic biomolecules including DNA and ionic peptide via the formation of soluble interpolyelectrolyte complexes. The development of smart artificial chaperones that can be spatiotemporally controlled by a remotely guided signal would expand the functions of artificial chaperones. Herein, to enable photocontrol of chaperone activity, a cationic comb-type copolymer bearing malachite green as a photoresponsive unit was designed. We first prepared a series of carboxylic acid derivatives of malachite green identified a derivative that could be quickly and quantitatively converted to the cationic form from the nonionic form by photoirradiation. This derivative was conjugated to the cationic comb-type copolymer, poly(allylamine)-graft-poly(ethylene glycol) through a condensation reaction. Upon photoirradiation, the copolymer bearing 9 mol% malachite green enhanced the membrane disruptive activity of acidic peptide E5 and induced morphological changes in liposomes. This demonstration of photoresponsive activation of chaperoning activity of a copolymer suggests that the installation of carboxyl derivatives of malachite green will impart photoresponsiveness to various materials including biopolymers.
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Affiliation(s)
- Seiya Takemura
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Wang J, Raito H, Shimada N, Maruyama A. A Cationic Copolymer Enhances Responsiveness and Robustness of DNA Circuits. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304091. [PMID: 37340578 DOI: 10.1002/smll.202304091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/12/2012] [Indexed: 06/22/2023]
Abstract
Toehold-mediated DNA circuits are extensively employed to construct diverse DNA nanodevices and signal amplifiers. However, operations of these circuits are slow and highly susceptive to molecular noise such as the interference from bystander DNA strands. Herein, this work investigates the effects of a series of cationic copolymers on DNA catalytic hairpin assembly, a representative toehold-mediated DNA circuit. One copolymer, poly(L -lysine)-graft-dextran, significantly enhances the reaction rate by 30-fold due to its electrostatic interaction with DNA. Moreover, the copolymer considerably alleviates the circuit's dependency on the length and GC content of toehold, thereby enhancing the robustness of circuit operation against molecular noise. The general effectiveness of poly(L -lysine)-graft-dextran is demonstrated through kinetic characterization of a DNA AND logic circuit. Therefore, use of a cationic copolymer is a versatile and efficient approach to enhance the operation rate and robustness of toehold-mediated DNA circuits, paving the way for more flexible design and broader application.
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Affiliation(s)
- Jun Wang
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama, 226-8501, Japan
| | - Hayashi Raito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama, 226-8501, Japan
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Nie L, Zeng X, Hongbo L, Wang S, Lu Z, Yu R. Entropy-driven DNA circuit with two-stage strand displacement for elegant and robust detection of miRNA let-7a. Anal Chim Acta 2023; 1269:341392. [PMID: 37290851 DOI: 10.1016/j.aca.2023.341392] [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: 12/27/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) research in cancer diagnosis is expanding, on account of miRNAs were demonstrated to be key indicator of gene expression and hopeful candidates for biomarkers. In this study, a stable miRNA-let-7a fluorescent biosensor was successfully designed based on an exonuclease Ⅲ-assisted two-stage strand displacement reaction (SDR). First, an entropy-driven SDR containing a three-chain structure of the substrate is used in our designed biosensor, leading to reduce the reversibility of the target recycling process in each step. The target acts on the first stage to start the entropy-driven SDR, which generates the trigger used to stimulate the exonuclease Ⅲ-assisted SDR in the second stage. At the same time, we design a SDR one-step amplification strategy as a comparison. Expectly, this developed two-stage strand displacement system has a low detection limit of 25.0 pM as well as a broad detection range of 4 orders of magnitude, making it more sensitive than the SDR one-step sensor, whose detection limit is 0.8 nM. In addition, this sensor has high specificity across members of the miRNA family. Therefore, we can take advantage of this biosensor to promote miRNA research in cancer diagnosis sensing systems.
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Affiliation(s)
- Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Xiaogang Zeng
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Li Hongbo
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Zhanghui Lu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
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Chen Q, Wu L, Zhao F, Liu B, Wu Z, Yu R. Construction of hybridization chain reaction induced optical signal directed change of photonic crystals-DNA hydrogel sensor and its visual determination for aflatoxin B1. Food Chem 2023; 418:135891. [PMID: 36965395 DOI: 10.1016/j.foodchem.2023.135891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/27/2023]
Abstract
Herein, we have introduced hybridization chain reaction (HCR) into the photonic crystals (PhCs) hydrogel, for the first time, realizing HCR for inducing the change of the optical signal of PhCs hydrogel and using this hydrogel as a sensor for determination of the aflatoxin B1 (AFB1). By using specific sequences as the cross-linker, the extension of the cross-linker by HCR drives the swelling of the hydrogel, and the optical property of 2D PhCs array converts this swelling into a change of the Debye diffraction ring. Moreover, by further selecting the aptamer to construct the cross-linker, the hydrogel is also endowed with a unique capability for AFB1, making the hydrogel a novel sensor based on the signal amplification strategy. The results show that the designed hairpin DNAs can effectively trigger the HCR and cause the swelling of hydrogel, and the hydrogel sensor has a good determination performance and high specific recognition for AFB1.
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Affiliation(s)
- Qianshan Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Lingfeng Wu
- Leicester International Institute, Dalian University of Technology, Panjin 124221, People's Republic of China
| | - Feng Zhao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Bing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Zhaoyang Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China.
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
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Programming DNA Reaction Networks Using Allosteric DNA Hairpins. Biomolecules 2023; 13:biom13030481. [PMID: 36979416 PMCID: PMC10046357 DOI: 10.3390/biom13030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
The construction of DNA reaction networks with complex functions using various methods has been an important research topic in recent years. Whether the DNA reaction network can perform complex tasks and be recycled directly affects the performance of the reaction network. Therefore, it is very important to design and implement a DNA reaction network capable of multiple tasks and reversible regulation. In this paper, the hairpin allosteric method was used to complete the assembly task of different functional nucleic acids. In addition, information conversion of the network was realized. In this network, multiple hairpins were assembled into nucleic acid structures with different functions to achieve different output information through the cyclic use of trigger strands. A method of single-input dual-output information conversion was proposed. Finally, the network with signal amplification and reversible regulation was constructed. In this study, the reversible regulation of different functional nucleic acids in the same network was realized, which shows the potential of this network in terms of programmability and provides new ideas for constructing complex and multifunctional DNA reaction networks.
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