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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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Liang Z, Hu Y, Li CY, Yau WL, Tan K, Kuang Y. VPg-based bidirectional synthetic mRNA circuits enable orthogonal protein regulation for high-resolution cell separation. Chem Commun (Camb) 2024; 60:5427-5430. [PMID: 38685869 DOI: 10.1039/d4cc01725k] [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: 05/02/2024]
Abstract
Synthetic mRNA circuits commonly sense input to produce binary output signals for cell separation. Based on virus-origin cap-independent translation initiation machinery and RBP-aptamer interaction, we designed smart synthetic mRNA-based circuits that sense single input molecules to bidirectionally tune output signals in an orthogonal manner, enabling high-resolution separation of cell populations.
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Affiliation(s)
- Zhenghua Liang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Yaxin Hu
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Wai Laam Yau
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Kaixin Tan
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Yi Kuang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
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Liang Z, Tan K, Yin Li C, Kuang Y. Self-feedback loop-containing synthetic mRNA switches for controlled microRNA sensing. Bioorg Chem 2024; 144:107081. [PMID: 38232686 DOI: 10.1016/j.bioorg.2023.107081] [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: 10/30/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
Synthetic mRNA switches are powerful cell fate manipulation tools that sense cellular input molecules to directly control protein expression at the translational level. The lack of available switch designs that can mimic the natural sophisticated protein regulation is a fundamental issue that limits the application of synthetic mRNA switches. Here we report a new set of synthetic mRNA switches by incorporating self-feedback loop machineries to dynamically control protein expression levels upon sensing cellular microRNAs. We redesigned the coding region of the switch to express output protein along with mRNA regulatory proteins. RNA-binding proteins (RBPs) and RBP-binding RNA motifs (aptamers) guide the regulatory proteins to act on their own mRNAs, enhancing or flattening the effect of microRNA sensing. Importantly, we demonstrated that the switches with the positive feedback feature can enlarge a high-or-low microRNA effect into a nearly all-or-none pattern, substantially boosting the use of synthetic mRNA switches as high-performance microRNA sensors or binary cell regulation tools. We believe these novel mRNA switch designs provide new strategies to construct complex mRNA-based genetic circuits for future molecular sensing and cell engineering.
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Affiliation(s)
- Zhenghua Liang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region
| | - Kaixin Tan
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region
| | - Yi Kuang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region.
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Hu Y, Li CY, Lu Q, Kuang Y. Multiplex miRNA reporting platform for real-time profiling of living cells. Cell Chem Biol 2024; 31:150-162.e7. [PMID: 38035883 DOI: 10.1016/j.chembiol.2023.11.002] [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: 06/20/2023] [Revised: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
Accurately characterizing cell types within complex cell structures provides invaluable information for comprehending the cellular status during biological processes. In this study, we have developed an miRNA-switch cocktail platform capable of reporting and tracking the activities of multiple miRNAs (microRNAs) at the single-cell level, while minimizing disruption to the cell culture. Drawing on the principles of traditional miRNA-sensing mRNA switches, our platform incorporates subcellular tags and employs intelligent engineering to segment three subcellular regions using two fluorescent proteins. These designs enable the quantification of multiple miRNAs within the same cell. Through our experiments, we have demonstrated the platform's ability to track marker miRNA levels during cell differentiation and provide spatial information of heterogeneity on outlier cells exhibiting extreme miRNA levels. Importantly, this platform offers real-time and in situ miRNA reporting, allowing for multidimensional evaluation of cell profile and paving the way for a comprehensive understanding of cellular events during biological processes.
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Affiliation(s)
- Yaxin Hu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Qiuyu Lu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yi Kuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.
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Tan K, Hu Y, Liang Z, Li CY, Yau WL, Kuang Y. Dual Input-Controlled Synthetic mRNA Circuit for Bidirectional Protein Expression Regulation. ACS Synth Biol 2023; 12:2516-2523. [PMID: 37652441 PMCID: PMC10510700 DOI: 10.1021/acssynbio.3c00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Indexed: 09/02/2023]
Abstract
Synthetic mRNA circuits manipulate cell fate by controlling output protein expression via cell-specific input molecule detection. Most current circuits either repress or enhance output production upon input binding. Such binary input-output mechanisms restrict the fine-tuning of protein expression to control complex cellular events. Here we designed mRNA circuits using enhancer/repressor modules that were independently controlled by different input molecules, resulting in bidirectional output regulation; the maximal enhancement over maximal repression was 57 fold. The circuit either enhances or represses protein production in different cells based on the difference in the expression of two microRNAs. This study examined novel bidirectional circuit designs capable of fine-tuning protein production by sensing multiple input molecules. It also broadened the scope of cell manipulation by synthetic mRNA circuits, facilitating the development of mRNA circuits for precise cell manipulation and providing cell-based solutions to biomedical problems.
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Affiliation(s)
- Kaixin Tan
- Department
of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Building, Clear
Water Bay, Kowloon, Hong Kong
| | - Yaxin Hu
- Department
of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Building, Clear
Water Bay, Kowloon, Hong Kong
| | - Zhenghua Liang
- Department
of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Building, Clear
Water Bay, Kowloon, Hong Kong
| | - Cheuk Yin Li
- Department
of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Building, Clear
Water Bay, Kowloon, Hong Kong
| | - Wai Laam Yau
- Department
of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Building, Clear
Water Bay, Kowloon, Hong Kong
| | - Yi Kuang
- Department
of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Building, Clear
Water Bay, Kowloon, Hong Kong
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