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Chen K, Zhu L, Li J, Zhang Y, Yu Y, Wang X, Wei W, Huang K, Xu W. High-content tailoring strategy to improve the multifunctionality of functional nucleic acids. Biosens Bioelectron 2024; 261:116494. [PMID: 38901394 DOI: 10.1016/j.bios.2024.116494] [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: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yongxia Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wei Wei
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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2
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Yan H, Cao G, Wang J, Zhu X, Dong S, Huang Y, Chao M, Li Y, Gao F, Hua L. An enzymatically activated AND-gate DNA logic circuit for tumor cells recognition via multi-microRNAs detection. Biosens Bioelectron 2024; 256:116278. [PMID: 38608497 DOI: 10.1016/j.bios.2024.116278] [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: 12/29/2023] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
The DNA-based logic circuit, constructed to mimic biochemical reaction networks, is highly significant in detecting biomarkers at the molecular level. The differences in the expression levels of microRNAs (miRNAs) within different types of cells provide hope for distinguishing cell subtypes. However, reliance on a single miRNA often leads to unreliable results. Herein, we constructed an enzyme-triggered cascade logic circuit based on the AND gate, which is capable of generating corresponding fluorescence signals in the presence of target miRNAs. The introduction of apurinic/apyrimidinic (AP) sites effectively reduces the likelihood of false signal generation. Amplification of the fluorescence signal relies on the catalytic hairpin assembly and the repetitive reuse of the multicomponent nucleic acid enzyme (MNAzyme). We demonstrated that the logic circuit can not only distinguish cancer cells from normal cells but also identify different types of cancer cells. The programmability of the logic circuits and the simplicity of the assay system allow us to modify the functional sequences to recognize different types of biomarkers, thus providing a reference for the identification of various cell subtypes.
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Affiliation(s)
- Hanrong Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Guojun Cao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China; Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xu Zhu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Shuqing Dong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yuqi Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Minghao Chao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yuting Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Lei Hua
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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Lei Y, Li C, Ji X, Sun H, Liu X, Mao Z, Chen W, Qing Z, Liu J. Lowering Entropic Barriers in Triplex DNA Switches Facilitating Biomedical Applications at Physiological pH. Angew Chem Int Ed Engl 2024; 63:e202402123. [PMID: 38453654 DOI: 10.1002/anie.202402123] [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: 01/30/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/09/2024]
Abstract
Triplex DNA switches are attractive allosteric tools for engineering smart nanodevices, but their poor triplex-forming capacity at physiological conditions limited the practical applications. To address this challenge, we proposed a low-entropy barrier design to facilitate triplex formation by introducing a hairpin duplex linker into the triplex motif, and the resulting triplex switch was termed as CTNSds. Compared to the conventional clamp-like triplex switch, CTNSds increased the triplex-forming ratio from 30 % to 91 % at pH 7.4 and stabilized the triple-helix structure in FBS and cell lysate. CTNSds was also less sensitive to free-energy disturbances, such as lengthening linkers or mismatches in the triple-helix stem. The CTNSds design was utilized to reversibly isolate CTCs from whole blood, achieving high capture efficiencies (>86 %) at pH 7.4 and release efficiencies (>80 %) at pH 8.0. Our approach broadens the potential applications of DNA switches-based switchable nanodevices, showing great promise in biosensing and biomedicine.
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Affiliation(s)
- Yanli Lei
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Chuangchuang Li
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xinyue Ji
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Haiyan Sun
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xiaowen Liu
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, 410083, China
| | - Zenghui Mao
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, 410083, China
| | - Weiju Chen
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2 L 3G1, Canada
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Qi M, Shi P, Zhang X, Cui S, Liu Y, Zhou S, Zhang Q. Reconfigurable DNA triplex structure for pH responsive logic gates †. RSC Adv 2023; 13:9864-9870. [PMID: 36998523 PMCID: PMC10043996 DOI: 10.1039/d3ra00536d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C+ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks. We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.![]()
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Affiliation(s)
- Mingxuan Qi
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
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Wang L, Xu M, Zhou H, Yan K, Duan S, Xue D, Wang Y, Di B, Hu C. Teaching PCR for Simultaneous Sensing of Gene Transcription and Downstream Metabolites by Cucurbit[8]uril-Mediated Intervention of Polymerase Activity. Anal Chem 2022; 94:8715-8723. [PMID: 35671188 DOI: 10.1021/acs.analchem.2c01103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The target of typical PCR analysis is restricted to nucleic acids. To this end, we report here a novel strategy to simultaneously detect genetic and metabolic markers using commercial PCR kits with cucurbit[8]urils (CB[8]) implemented to manipulate the activity of Taq DNA polymerase. CB[8] binds with the nonionic surfactants and displaces them from the polymerase surface, resulting in decreased enzyme activity. Meanwhile, the inhibited enzyme can be reversibly activated when spermine, the downstream metabolite of ornithine decarboxylase (ODC), is present in the sample, which competitively binds to CB[8] and recovers polymerase activity. CB[8] was implemented in conventional PCR kits not only to reduce false-positive results but also to extend the detection range of PCR technology. With this novel method to detect ODC in cell lysates containing both the nucleotides and intracellular metabolites, positive results were only observed in highly active HEK 293T cells, whereas silent cells treated with ODC inhibitor showed negative readouts, therefore providing a simple but elegant dual-modality PCR method for precision diagnosis.
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Affiliation(s)
- Lancheng Wang
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Mingjie Xu
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Huimin Zhou
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Kun Yan
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Shiqi Duan
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Dandan Xue
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Youmei Wang
- Key Laboratory of Drug Monitoring and Control, Drug Intelligence and Forensic Center, Ministry of Public Security, No. 18 Dongbeiwang West Road, Beijing 100193, China
| | - Bin Di
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Chi Hu
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
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Lin PY, Chi R, Wu YL, Ho JAA. Applications of triplex DNA nanostructures in sensor development. Anal Bioanal Chem 2022; 414:5217-5237. [PMID: 35469098 DOI: 10.1007/s00216-022-04058-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022]
Abstract
Triplex DNA nanostructures are one of the most emerging and fascinating self-assembled nanostructures due to their unique nanoparticle-like organization and inherit characteristics. They have attracted numerous interests recently because of their versatile and powerful utility in diverse areas of science and technology, such as clinical or disease diagnosis and stimuli-based drug delivery. This review addresses particularly the utilization of DNA triplexes in the development of biosensors for detecting nucleic acid; strategies in sensing pH, protein activity, ions, or molecules. Finally, an outlook for potential applications of triplex DNA nanoswitches is provided.
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Affiliation(s)
- Pei-Ying Lin
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Rong Chi
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Ling Wu
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Ja-An Annie Ho
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Biotechnology, National Taiwan University, Taipei, 10617, Taiwan.
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Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F. Protein–Protein Communication Mediated by an Antibody‐Responsive DNA Nanodevice**. Angew Chem Int Ed Engl 2022; 61:e202115680. [DOI: 10.1002/anie.202115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Simona Ranallo
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Daniela Sorrentino
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health Istituto Superiore di Sanità Viale Regina Elena 299 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F. Protein–Protein Communication Mediated by an Antibody‐Responsive DNA Nanodevice**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simona Ranallo
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Daniela Sorrentino
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health Istituto Superiore di Sanità Viale Regina Elena 299 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara CA 93106 USA
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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Wang Y, Ji H, Wang Y, Sun J. Stability Based on PI Control of Three-Dimensional Chaotic Oscillatory System via DNA Chemical Reaction Networks. IEEE Trans Nanobioscience 2021; 20:311-322. [PMID: 33835920 DOI: 10.1109/tnb.2021.3072047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The classical proportional integral (PI) controller of SISO linear system is realized by DNA chemical reaction networks (CRNs) in the previous work. Up to now, few works have been done to realize PI controller of chaotic system through DNA CRNs. In this paper, a three-dimensional chaotic oscillatory system and a PI controller of three-dimensional chaotic oscillatory system are proposed by DNA CRNs. The CRNs of chaotic oscillatory system are made up of catalysis modules, degradation module and annihilation module then chemical reaction equations can be compiled into three-dimensional chaotic oscillatory system by the law of mass action to generate chaotic oscillatory signals. The CRNs of PI controller are designed by an integral module, a proportion module and an addition module, which can be compiled into PI controller for stabilizing chaotic oscillatory signals. The simulations of Matlab and Visual DSD are given to show our design achieving the PI control of a three-variable chaotic oscillatory system.
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Development of Specific Inhibitors for Oncogenic Phosphatase PPM1D by Using Ion-Responsive DNA Aptamer Library. Catalysts 2020. [DOI: 10.3390/catal10101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
(1) Background: Ser/Thr protein phosphatase PPM1D is an oncogenic protein. In normal cells, however, PPM1D plays essential roles in spermatogenesis and immune response. Hence, it is necessary to develop novel PPM1D inhibitors without side effects on normal cells. Stimuli-responsive molecules are suitable for the spatiotemporal regulation of inhibitory activity. (2) Methods: In this study, we designed an ion-responsive DNA aptamer library based on G-quadruplex DNA that can change its conformation and function in response to monovalent cations. (3) Results: Using this library, we identified the PPM1D specific inhibitor M1D-Q5F aptamer. The M1D-Q5F aptamer showed anti-cancer activity against breast cancer MCF7 cells. Interestingly, the induction of the structural change resulting in the formation of G-quadruplex upon stimulation by monovalent cations led to the enhancement of the inhibitory activity and binding affinity of M1D-Q5F. (4) Conclusions: These data suggest that the M1D-Q5F aptamer may act as a novel stimuli-responsive anti-cancer agent.
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