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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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Huang K, Song Q, Fang M, Yao D, Shen X, Xu X, Chen X, Zhu L, Yang Y, Ren A. Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift. Nat Chem Biol 2024:10.1038/s41589-024-01633-1. [PMID: 38816645 DOI: 10.1038/s41589-024-01633-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
RNA-based fluorogenic modules have revolutionized the spatiotemporal localization of RNA molecules. Recently, a fluorophore named 5-((Z)-4-((2-hydroxyethyl)(methyl)amino)benzylidene)-3-methyl-2-((E)-styryl)-3,5-dihydro-4H-imidazol-4-one (NBSI), emitting in red spectrum, and its cognate aptamer named Clivia were identified, exhibiting a large Stokes shift. To explore the underlying molecular basis of this unique RNA-fluorophore complex, we determined the tertiary structure of Clivia-NBSI. The overall structure uses a monomeric, non-G-quadruplex compact coaxial architecture, with NBSI sandwiched at the core junction. Structure-based fluorophore recognition pattern analysis, combined with fluorescence assays, enables the orthogonal use of Clivia-NBSI and other fluorogenic aptamers, paving the way for both dual-emission fluorescence and bioluminescence imaging of RNA molecules within living cells. Furthermore, on the basis of the structure-based substitution assay, we developed a multivalent Clivia fluorogenic aptamer containing multiple minimal NBSI-binding modules. This innovative design notably enhances the recognition sensitivity of fluorophores both in vitro and in vivo, shedding light on future efficient applications in various biomedical and research contexts.
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Affiliation(s)
- Kaiyi Huang
- Department of Cardiology, The Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Mengyue Fang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Deqiang Yao
- Institute of Aging and Tissue Regeneration, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xianjun Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Linyong Zhu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Aiming Ren
- Department of Cardiology, The Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China.
- Life Sciences Institute, Zhejiang University, Hangzhou, China.
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3
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Zuo F, Jiang L, Su N, Zhang Y, Bao B, Wang L, Shi Y, Yang H, Huang X, Li R, Zeng Q, Chen Z, Lin Q, Zhuang Y, Zhao Y, Chen X, Zhu L, Yang Y. Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA. Nat Chem Biol 2024:10.1038/s41589-024-01629-x. [PMID: 38783134 DOI: 10.1038/s41589-024-01629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.
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Affiliation(s)
- Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yaqiang Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Limei Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yajie Shi
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huimin Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinyi Huang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ruilong Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qingmei Zeng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yingping Zhuang
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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Zhang Y, Xu Z, Xiao Y, Jiang H, Zuo X, Li X, Fang X. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST. Nat Commun 2024; 15:4206. [PMID: 38760339 PMCID: PMC11101630 DOI: 10.1038/s41467-024-48478-9] [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: 10/02/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore-quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric "A"-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore-quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST-tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.
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Affiliation(s)
- Yufan Zhang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China
| | - Zhonghe Xu
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Xiao
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haodong Jiang
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Xing Li
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Xianyang Fang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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5
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Gu Y, Bai R, Qiu X, Wang X, Lu S, Li CM, Guo C. In Vivo Imaging MicroRNA with Bright Fluorescent RNA Aptamer Through Target-Mediated Entropy-Driven Toehold Exchange. Anal Chem 2024; 96:7609-7617. [PMID: 38687631 DOI: 10.1021/acs.analchem.4c00510] [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
MicroRNAs (miRNAs) play vital roles in biological activities, but their in vivo imaging is still challenging due to the low abundance and the lack of efficient fluorescent tools. RNA aptamers with high affinity and low background emerge for bioimaging yet suffering from low brightness. We introduce a rational design based on target-mediated entropy-driven toehold exchange (EDTE) to induce the release of RNA aptamer and subsequently light up corresponding fluorophore, which achieves selective imaging of miRNAs with good stability in both living cells and tumor-bearing mouse. Through tailoring recognition unit of the EDTE probes, highly sensitive imaging of different miRNAs including miRNA-125b and miRNA-21 is achieved, confirming its universal bioimaging applications. In comparison with the reported "one-to-one" model, the EDTE strategy shows a remarkable 4.6-time improvement in signal/noise ratio for intracellular imaging of the same miRNA. Particularly, it realizes sensitive imaging of miRNA in vivo, providing a promising tool in investigating functions and interactions of disease-associated miRNAs.
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Affiliation(s)
- Yu Gu
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Rui Bai
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Xingchen Qiu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Xuefu Road, Suzhou 215009, P. R. China
| | - Xiaobao Wang
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Shasha Lu
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Chang-Ming Li
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Chunxian Guo
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
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6
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Park SV, Kang B, Lee M, Yoo H, Jo H, Woo S, Oh SS. In vitro selection of a trans aptamer complex for target-responsive fluorescence activation. Anal Chim Acta 2024; 1301:342465. [PMID: 38553123 DOI: 10.1016/j.aca.2024.342465] [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: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions. RESULTS By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges. SIGNIFICANCE This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.
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Affiliation(s)
- Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Minjong Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sungwook Woo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
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7
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Gu Y, Fan C, Yang H, Sun H, Wang X, Qiu X, Chen B, Li CM, Guo C. Fluorogenic RNA Aptamer-Based Amplification and Transcription Strategy for Label-free Sensing of Methyltransferase Activity in Complex Matrixes. Adv Biol (Weinh) 2024; 8:e2300668. [PMID: 38327153 DOI: 10.1002/adbi.202300668] [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: 12/29/2023] [Indexed: 02/09/2024]
Abstract
DNA methyltransferase is significant in cellular activities and gene expression, and its aberrant expression is closely linked to various cancers during initiation and progression. Currently, there is a great demand for reliable and label-free techniques for DNA methyltransferase evaluation in tumor diagnosis and cancer therapy. Herein, a low-background fluorescent RNA aptamer-based sensing approach for label-free quantification of cytosine-guanine (CpG) dinucleotides methyltransferase (M.SssI) is reported. The fluorogenic light-up RNA aptamers-based strategy exhibits high selectivity via restriction endonuclease, padlock-based recognition, and RNA transcription. By combining rolling circle amplification (RCA), and RNA transcription with fluorescence response of RNA aptamers of Spinach-dye compound, the proposed platform exhibited efficiently ultrahigh sensitivity toward M.SssI. Eventually, the detection can be achieved in a linear range of 0.02-100 U mL-1 with a detection limit of 1.6 × 10-3 U mL-1. Owing to these superior features, the method is further applied in serum samples spiked M.SssI, which delivers a recovery ranging from 92.0 to 107.0% and a relative standard deviation <7.0%, providing a promising and practical tool for determining M.SssI in complex biological matrices.
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Affiliation(s)
- Yu Gu
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Cunxia Fan
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Hongbin Yang
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Huiping Sun
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Xiaobao Wang
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Xingchen Qiu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Bo Chen
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
- Jiangsu Key Laboratory for Biomaterials and Devices, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, 210009, P. R. China
| | - Chang-Ming Li
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Chunxian Guo
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
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8
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Ji R, Wang L, Shang Y, Du S, Xiao Y, Dong W, Cui L, Gao R, Ren K. RNA Condensate as a Versatile Platform for Improving Fluorogenic RNA Aptamer Properties and Cell Imaging. J Am Chem Soc 2024; 146:4402-4411. [PMID: 38329936 DOI: 10.1021/jacs.3c09162] [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: 02/10/2024]
Abstract
Fluorogenic RNA aptamers are valuable tools for cell imaging, but they still suffer from shortcomings such as easy degradation, limited photostability, and low fluorescence enhancement. Molecular crowding conditions enable the stabilization of the structure, promotion of folding, and improvement of activity of functional RNA. Based on artificial RNA condensates, here we present a versatile platform to improve fluorogenic RNA aptamer properties and develop sensors for target analyte imaging in living cells. Using the CUG repeat as a general tag to drive phase separation, various fluorogenic aptamer-based RNA condensates (FLARE) were prepared. We show that the molecular crowding of FLARE can improve the enzymatic resistance, thermostability, photostability, and binding affinity of fluorogenic RNA aptamers. Moreover, the FLARE systems can be modularly engineered into sensors (FLARES), which demonstrate enhanced brightness and sensitivity compared to free sensors dispersed in homogeneous solution. This scalable design principle provides new insights into RNA aptamer property regulation and cellular imaging.
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Affiliation(s)
- Ruoyang Ji
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Long Wang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Yuzhe Shang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Songyuan Du
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Yang Xiao
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Wei Dong
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P.R. China
| | - Ruru Gao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
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9
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Tang AA, Afasizheva A, Cano CT, Plath K, Black D, Franco E. Optimization of RNA Pepper Sensors for the Detection of Arbitrary RNA Targets. ACS Synth Biol 2024; 13:498-508. [PMID: 38295291 DOI: 10.1021/acssynbio.3c00426] [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] [Indexed: 02/02/2024]
Abstract
The development of fluorescent light-up RNA aptamers (FLAPs) has paved the way for the creation of sensors to track RNA in live cells. A major challenge with FLAP sensors is their brightness and limited signal-to-background ratio both in vivo and in vitro. To address this, we develop sensors using the Pepper aptamer, which exhibits superior brightness and photostability when compared to other FLAPs. The sensors are designed to fold into a low fluorescence conformation and to switch to a high fluorescence conformation through toehold or loop-mediated interactions with their RNA target. Our sensors detect RNA targets as short as 20 nucleotides in length with a wide dynamic range over 300-fold in vitro, and we describe strategies for optimizing the sensor's performance for any given RNA target. To demonstrate the versatility of our design approach, we generated Pepper sensors for a range of specific, biologically relevant RNA sequences. Our design and optimization strategies are portable to other FLAPs and offer a promising foundation for future development of RNA sensors with high specificity and sensitivity for detecting RNA biomarkers with multiple applications.
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Affiliation(s)
- Anli A Tang
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Kathrin Plath
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Douglas Black
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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10
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Fischermeier D, Steinmetzger C, Höbartner C, Mitrić R. Conformational preferences of modified nucleobases in RNA aptamers and their effect on Förster resonant energy transfer. Phys Chem Chem Phys 2023; 26:241-248. [PMID: 38054366 DOI: 10.1039/d3cp04704k] [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: 12/07/2023]
Abstract
Förster resonant energy transfer (FRET) can be utilized in the study of tertiary structures of RNA aptamers, which bind specific fluorophoric ligands to form a fluorogenic aptamer complex. By introducing the emissive nucleobase analog 4-cyanoindole into the fluorogenic Chili RNA aptamer a FRET pair was established. The interpretation of studies aiming to investigate those tertiary structures using FRET, however, relies on prior knowledge about conformational properties of the nucleobase, which govern exciton transfer capabilities. Herein we employed classical molecular dynamics combined with Förster exciton theory to elucidate the preferred orientation relative to proximate bases and the influence on exciton transfer efficiency in multiple substitution sites. We did this by comparing the chromophoric distances emergent from MD simulations with experimental FRET data based on structural data of the native aptamer. We present the outlined methodology as a means to reliably evaluate future nucleobase analogue candidates in terms of their structural behavior and emergent exciton transfer properties as exemplified in the study of the preferred orientation of 4-cyanoindole in the Chili RNA aptamer.
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Affiliation(s)
- David Fischermeier
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Christian Steinmetzger
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Claudia Höbartner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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11
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Yin P, Ge M, Xie S, Zhang L, Kuang S, Nie Z. A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers. Chem Sci 2023; 14:14131-14139. [PMID: 38098702 PMCID: PMC10717586 DOI: 10.1039/d3sc04957d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of gene expression at the post-transcriptional level, offering valuable insights into disease mechanisms and prospects for targeted therapeutic interventions. Herein, we present a class of miRNA-induced light-up RNA sensors (miLS) that are founded on the toehold mediated principle and employ the fluorogenic RNA aptamers Pepper and Squash as imaging modules. By incorporating a sensor switch to disrupt the stabilizing stem of these aptamers, our design offers enhanced flexibility and convertibility for different target miRNAs and aptamers. These sensors detect multiple miRNA targets (miR-21 and miR-122) with detection limits of 0.48 and 0.2 nM, respectively, while achieving a robust signal-to-noise ratio of up to 44 times. Capitalizing on the distinct fluorescence imaging channels afforded by Pepper-HBC620 (red) and Squash-DFHBI-1T (green), we establish an orthogonal miRNA activation imaging platform, enabling the simultaneous visualization of different intracellular miRNAs in living cells. Our dual-color orthogonal miLS imaging platform provides a powerful tool for sequence-specific miRNA imaging in different cells, opening up new avenues for studying the intricate functions of RNA in living cells.
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Affiliation(s)
- Peng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Mingmin Ge
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Li Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
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12
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Dodaro A, Pavan M, Menin S, Salmaso V, Sturlese M, Moro S. Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes. Front Mol Biosci 2023; 10:1294543. [PMID: 38028536 PMCID: PMC10679717 DOI: 10.3389/fmolb.2023.1294543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simulation times which hamper their conformational sampling capabilities. In the present work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of unbinding kinetics, to characterize RNA-ligand complexes. In this article, we explored its applicability as a post-docking refinement tool on RNA in complex with small molecules, highlighting the capability of this method to identify the native binding mode among a set of decoys across various pharmaceutically relevant test cases.
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Affiliation(s)
| | | | | | | | | | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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13
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Wang T, Simmel FC. Switchable Fluorescent Light-Up Aptamers Based on Riboswitch Architectures. Angew Chem Int Ed Engl 2023; 62:e202302858. [PMID: 37163453 DOI: 10.1002/anie.202302858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Fluorescent light-up RNA aptamers (FLAPs) such as Spinach or Mango can bind small fluorogens and activate their fluorescence. Here, we adopt a switching mechanism otherwise found in riboswitches and use it to engineer switchable FLAPs that can be activated or repressed by trigger oligonucleotides or small metabolites. The fluorophore binding pocket of the FLAPs comprises guanine (G) quadruplexes, whose critical nucleotides can be sequestered by corresponding anti-FLAP sequences, leading to an inactive conformation and thus preventing association with the fluorophore. We modified the FLAPs with designed toehold hairpins that carry either an anti-FLAP or an anti-anti-FLAP sequence within the loop region. The addition of an input RNA molecule triggers a toehold-mediated strand invasion process that refolds the FLAP into an active or inactive configuration. Several of our designs display close-to-zero leak signals and correspondingly high ON/OFF fluorescence ratios. We also modified purine aptamers to sequester a partial anti-FLAP or an anti-anti-FLAP sequence to control the formation of the fluorogen-binding conformation, resulting in FLAPs whose fluorescence is activated or deactivated in the presence of guanine or adenine. We demonstrate that switching modules can be easily combined to generate FLAPs whose fluorescence depends on several inputs with different types of input logic.
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Affiliation(s)
- Tianhe Wang
- Physics of Synthetic Biological Systems-E14, Department of Bioscience, TUM School of Natural Science, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems-E14, Department of Bioscience, TUM School of Natural Science, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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14
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Herrera-Gutierrez J, Burden SJ, Kobernat SE, Shults NH, Smith M, Fologea D, Hayden EJ. Double-stemmed and split structural variants of fluorescent RNA Mango aptamers. RNA (NEW YORK, N.Y.) 2023; 29:1355-1364. [PMID: 37268327 PMCID: PMC10573287 DOI: 10.1261/rna.079651.123] [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: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 06/04/2023]
Abstract
Aptamers with fluorogenic ligands are emerging as useful tools to quantify and track RNA molecules. The RNA Mango family of aptamers have a useful combination of tight ligand binding, bright fluorescence, and small size. However, the simple structure of these aptamers, with a single base-paired stem capped by a G-quadruplex, can limit the sequence and structural modifications needed for many use-inspired designs. Here we report new structural variants of RNA Mango that have two base-paired stems attached to the quadruplex. Fluorescence saturation analysis of one of the double-stemmed constructs showed a maximum fluorescence that is ∼75% brighter than the original single-stemmed Mango I. A small number of mutations to nucleotides in the tetraloop-like linker of the second stem were subsequently analyzed. The effect of these mutations on the affinity and fluorescence suggested that the nucleobases of the second linker do not directly interact with the fluorogenic ligand (TO1-biotin), but may instead induce higher fluorescence by indirectly altering the ligand properties in the bound state. The effects of the mutations in this second tetraloop-like linker indicate the potential of this second stem for rational design and reselection experiments. Additionally, we demonstrated that a bimolecular mango designed by splitting the double-stemmed Mango can function when two RNA molecules are cotranscribed from different DNA templates in a single in vitro transcription. This bimolecular Mango has potential application in detecting RNA-RNA interactions. Together, these constructs expand the designability of the Mango aptamers to facilitate future applications of RNA imaging.
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Affiliation(s)
| | - Steven J Burden
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
| | - Sarah E Kobernat
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas H Shults
- Department of Biological Sciences, Boise State University, Boise, Idaho 83725, USA
| | - Mark Smith
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
| | - Daniel Fologea
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
- Department of Physics, Boise State University, Boise, Idaho 83725, USA
| | - Eric J Hayden
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
- Department of Biological Sciences, Boise State University, Boise, Idaho 83725, USA
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15
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Deng J, Fang X, Huang L, Li S, Xu L, Ye K, Zhang J, Zhang K, Zhang QC. RNA structure determination: From 2D to 3D. FUNDAMENTAL RESEARCH 2023; 3:727-737. [PMID: 38933295 PMCID: PMC11197651 DOI: 10.1016/j.fmre.2023.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2024] Open
Abstract
RNA molecules serve a wide range of functions that are closely linked to their structures. The basic structural units of RNA consist of single- and double-stranded regions. In order to carry out advanced functions such as catalysis and ligand binding, certain types of RNAs can adopt higher-order structures. The analysis of RNA structures has progressed alongside advancements in structural biology techniques, but it comes with its own set of challenges and corresponding solutions. In this review, we will discuss recent advances in RNA structure analysis techniques, including structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering. Often, a combination of multiple techniques is employed for the integrated analysis of RNA structures. We also survey important RNA structures that have been recently determined using various techniques.
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Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xianyang Fang
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lilei Xu
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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16
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Kotwal SB, Orekondey N, Saradadevi GP, Priyadarshini N, Puppala NV, Bhushan M, Motamarry S, Kumar R, Mohannath G, Dey RJ. Multidimensional futuristic approaches to address the pandemics beyond COVID-19. Heliyon 2023; 9:e17148. [PMID: 37325452 PMCID: PMC10257889 DOI: 10.1016/j.heliyon.2023.e17148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023] Open
Abstract
Globally, the impact of the coronavirus disease 2019 (COVID-19) pandemic has been enormous and unrelenting with ∼6.9 million deaths and ∼765 million infections. This review mainly focuses on the recent advances and potentially novel molecular tools for viral diagnostics and therapeutics with far-reaching implications in managing the future pandemics. In addition to briefly highlighting the existing and recent methods of viral diagnostics, we propose a couple of potentially novel non-PCR-based methods for rapid, cost-effective, and single-step detection of nucleic acids of viruses using RNA mimics of green fluorescent protein (GFP) and nuclease-based approaches. We also highlight key innovations in miniaturized Lab-on-Chip (LoC) devices, which in combination with cyber-physical systems, could serve as ideal futuristic platforms for viral diagnosis and disease management. We also discuss underexplored and underutilized antiviral strategies, including ribozyme-mediated RNA-cleaving tools for targeting viral RNA, and recent advances in plant-based platforms for rapid, low-cost, and large-scale production and oral delivery of antiviral agents/vaccines. Lastly, we propose repurposing of the existing vaccines for newer applications with a major emphasis on Bacillus Calmette-Guérin (BCG)-based vaccine engineering.
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Affiliation(s)
- Shifa Bushra Kotwal
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | - Nidhi Orekondey
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | | | - Neha Priyadarshini
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | - Navinchandra V Puppala
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | - Mahak Bhushan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, West Bengal 741246, India
| | - Snehasri Motamarry
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | - Rahul Kumar
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | - Gireesha Mohannath
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
| | - Ruchi Jain Dey
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Telangana 500078, India
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17
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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18
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Passalacqua LFM, Starich MR, Link KA, Wu J, Knutson JR, Tjandra N, Jaffrey SR, Ferré-D'Amaré AR. Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun 2023; 14:2969. [PMID: 37221204 PMCID: PMC10205801 DOI: 10.1038/s41467-023-38683-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.
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Affiliation(s)
- Luiz F M Passalacqua
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary R Starich
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katie A Link
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiahui Wu
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
- Department of Chemistry, Binghamton University, Binghamton, NY, 13902, USA
| | - Jay R Knutson
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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19
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Sharon JA, Dasrath C, Fujiwara A, Snyder A, Blank M, O'Brien S, Aufdembrink LM, Engelhart AE, Adamala KP. Trumpet is an operating system for simple and robust cell-free biocomputing. Nat Commun 2023; 14:2257. [PMID: 37080970 PMCID: PMC10119096 DOI: 10.1038/s41467-023-37752-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
Biological computation is becoming a viable and fast-growing alternative to traditional electronic computing. Here we present a biocomputing technology called Trumpet: Transcriptional RNA Universal Multi-Purpose GatE PlaTform. Trumpet combines the simplicity and robustness of the simplest in vitro biocomputing methods, adding signal amplification and programmability, while avoiding common shortcomings of live cell-based biocomputing solutions. We have demonstrated the use of Trumpet to build all universal Boolean logic gates. We have also built a web-based platform for designing Trumpet gates and created a primitive processor by networking several gates as a proof-of-principle for future development. The Trumpet offers a change of paradigm in biocomputing, providing an efficient and easily programmable biological logic gate operating system.
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Affiliation(s)
- Judee A Sharon
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Chelsea Dasrath
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Aiden Fujiwara
- Department of Computer Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Alessandro Snyder
- Department of Computer Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Mace Blank
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Sam O'Brien
- Department of Computer Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Lauren M Aufdembrink
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Aaron E Engelhart
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA.
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20
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Huang Z, Guo X, Ma X, Wang F, Jiang JH. Genetically encodable tagging and sensing systems for fluorescent RNA imaging. Biosens Bioelectron 2023; 219:114769. [PMID: 36252312 DOI: 10.1016/j.bios.2022.114769] [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: 07/31/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 10/06/2022]
Abstract
Live cell imaging of RNAs is crucial to interrogate their fundamental roles in various biological processes. The highly spatiotemporal dynamic nature of RNA abundance and localization has presented great challenges for RNA imaging. Genetically encodable tagging and sensing (GETS) systems that can be continuously produced in living systems have afforded promising tools for imaging and sensing RNA dynamics in live cells. Here we review the recent advances of GETS systems that have been developed for RNA tagging and sensing in live cells. We first describe the various GETS systems using MS2-bacteriophage-MS2 coat protein, pumilio homology domain and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9/13 for RNA labeling and tracking. The progresses of GETS systems for fluorogenic labeling and/or sensing RNAs by engineering light-up RNA aptamers, CRISPR-Cas9 systems and RNA aptamer stabilized fluorogenic proteins are then elaborated. The challenges and future perspectives in this field are finally discussed. With the continuing development, GETS systems will afford powerful tools to elucidate RNA biology in living systems.
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Affiliation(s)
- Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xiaoyan Guo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xianbo Ma
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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21
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Hou Q, Jaffrey SR. Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells. RNA Biol 2023; 20:198-206. [PMID: 37129556 PMCID: PMC10155629 DOI: 10.1080/15476286.2023.2206248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023] Open
Abstract
RNA aptamers are structured RNAs that can bind to diverse ligands, including proteins, metabolites, and other small molecules. RNA aptamers are widely used as in vitro affinity reagents. However, RNA aptamers have not been highly successful as bioactive intracellular molecules that can bind target molecules and influence cellular processes. We describe how poor RNA aptamer expression and especially poor RNA aptamer folding have limited the use of RNA aptamers in RNA synthetic biology applications. We discuss innovative new approaches that promote RNA aptamer folding in living cells and how these approaches have improved the function of aptamers in mammalian cells. These new approaches are making RNA aptamer-based synthetic biology and RNA aptamer therapeutic applications much more achievable.
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Affiliation(s)
- Qian Hou
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R. Jaffrey
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
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22
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Advances in
G
‐quadruplexes‐based fluorescent imaging. Biopolymers 2022; 113:e23528. [DOI: 10.1002/bip.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
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23
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Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA. Structural Basis for Fluorescence Activation by Pepper RNA. ACS Chem Biol 2022; 17:1866-1875. [PMID: 35759696 PMCID: PMC9969808 DOI: 10.1021/acschembio.2c00290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K+ dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg2+ ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.
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Affiliation(s)
- Huw C. Rees
- Department of Chemistry, University of Chicago, Chicago, Illinois, 60637, United States
| | - Wojciech Gogacz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States
| | - Joseph A. Piccirilli
- Department of Chemistry, University of Chicago, Chicago, Illinois, 60637, United States,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, United States,corresponding author
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24
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Spinach-based RNA mimicking GFP in plant cells. Funct Integr Genomics 2022; 22:423-428. [PMID: 35267109 PMCID: PMC9197860 DOI: 10.1007/s10142-022-00835-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 12/23/2022]
Abstract
Spinach RNA-mimicking GFP (S-RMG) has been successfully used to monitor cellular RNAs including microRNAs in bacterium, yeast, and human cells. However, S-RMG has not been established in plants. In this study, we found that like bacterial, yeast, and human cellular tRNAs, plant tRNAs such as tRNALys can protect and/or stabilize the Spinach RNA aptamer interaction with the fluorophore DFHBI enabling detectable levels of green fluorescence to be emitted. The tRNALys-Spinach-tRNALys, once delivered into "chloroplast-free" onion epidermal cells can emit strong green fluorescence in the presence of DFHBI. Our results demonstrate for the first time that Spinach-based RNA visualization has the potential for in vivo monitoring of RNAs in plant cells.
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25
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Anisuzzaman S, Geraskin IM, Ilgu M, Bendickson L, Kraus GA, Nilsen-Hamilton M. Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities. RNA (NEW YORK, N.Y.) 2022; 28:865-877. [PMID: 35351813 PMCID: PMC9074905 DOI: 10.1261/rna.079005.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/11/2022] [Indexed: 06/03/2023]
Abstract
The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand how nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI [(Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one] that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that polyfluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ∼40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual transition to a more defined structure for which the most likely driving force is an interaction of the gateway adenine with a nearby 2'OH group. These results suggest that polyfluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.
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Affiliation(s)
- Sharif Anisuzzaman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Ivan M Geraskin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Muslum Ilgu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Lee Bendickson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - George A Kraus
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Marit Nilsen-Hamilton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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26
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Xu G, Zhao J, Yu H, Wang C, Huang Y, Zhao Q, Zhou X, Li C, Liu M. Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer. J Am Chem Soc 2022; 144:7731-7740. [PMID: 35442665 DOI: 10.1021/jacs.2c00478] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg2+ and Na+ ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through π-π stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,Xi'an Modern Chemistry Research Institute, Xi'an, 710065, People's Republic of China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Chen Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yangyu Huang
- Shaoyang University, Shaoyang, 422000, People's Republic of China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
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27
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VarnBuhler BS, Moon J, Dey SK, Wu J, Jaffrey SR. Detection of SARS-CoV-2 RNA Using a DNA Aptamer Mimic of Green Fluorescent Protein. ACS Chem Biol 2022; 17:840-853. [PMID: 35341244 PMCID: PMC9780036 DOI: 10.1021/acschembio.1c00893] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA detection is important in diverse diagnostic and analytical applications. RNAs can be rapidly detected using molecular beacons, which fluoresce upon hybridizing to a target RNA but require oligonucleotides with complex fluorescent dye and quencher conjugations. Here, we describe a simplified method for rapid fluorescence detection of a target RNA using simple unmodified DNA oligonucleotides. To detect RNA, we developed Lettuce, a fluorogenic DNA aptamer that binds and activates the fluorescence of DFHBI-1T, an otherwise nonfluorescent molecule that resembles the chromophore found in green fluorescent protein. Lettuce was selected from a randomized DNA library based on binding to DFHBI-agarose. We further show that Lettuce can be split into two separate oligonucleotide components, which are nonfluorescent on their own but become fluorescent when their proximity is induced by a target RNA. We designed several pairs of split Lettuce fragments that contain an additional 15-20 nucleotides that are complementary to adjacent regions of the SARS-CoV-2 RNA, resulting in Lettuce fluorescence only in the presence of the viral RNA. Overall, these studies describe a simplified RNA detection approach using fully unmodified DNA oligonucleotides that reconstitute the Lettuce aptamer templated by RNA.
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Affiliation(s)
- Bria S. VarnBuhler
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA,Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jared Moon
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Sourav Kumar Dey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Jiahui Wu
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY 10065, USA,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
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28
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Wu J, Svensen N, Song W, Kim H, Zhang S, Li X, Jaffrey SR. Self-Assembly of Intracellular Multivalent RNA Complexes Using Dimeric Corn and Beetroot Aptamers. J Am Chem Soc 2022; 144:5471-5477. [PMID: 35294188 PMCID: PMC9747565 DOI: 10.1021/jacs.1c13583] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA and RNA can spontaneously self-assemble into various structures, including aggregates, complexes, and ordered structures. The self-assembly reactions cannot be genetically encoded to occur in living mammalian cells since the double-stranded nucleic acids generated by current self-assembly approaches are unstable and activate innate RNA immunity pathways. Here, we show that recently described dimeric aptamers can be used to create RNAs that self-assemble and create RNA and RNA-protein assemblies in cells. We find that incorporation of five copies of Corn, a dimeric fluorogenic RNA aptamer, into an RNA causes the RNA to form large clusters in cells, reflecting multivalent RNA-RNA interactions enabled by these RNAs. Here, we also describe a second dimeric fluorogenic aptamer, Beetroot, which shows partial sequence similarity to Corn. Both Corn and Beetroot form homodimers with themselves but do not form Corn-Beetroot heterodimers. We thus use Corn and Beetroot to encode distinct RNA-protein assemblies in the same cells. Overall, these studies provide an approach for inducing RNA self-assembly, enable multiplexing of distinct RNA assemblies in cells, and demonstrate that proteins can be recruited to RNA assemblies to genetically encode intracellular RNA-protein assemblies.
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Affiliation(s)
| | | | - Wenjiao Song
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Hyaeyeong Kim
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Sulei Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xing Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Samie R. Jaffrey
- Corresponding Author: Samie R. Jaffrey – Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States,
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29
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Hyun Lee K, Kimoto M, Kawai G, Okamoto I, Fin A, Hirao I. Dye‐Conjugated Spinach RNA by Genetic Alphabet Expansion. Chemistry 2022; 28:e202104396. [DOI: 10.1002/chem.202104396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Kyung Hyun Lee
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Gota Kawai
- Chiba Institute of Technology (CIT) Tsudanuma 2-17-1 Narashino Chiba 275-0016 Japan
| | - Itaru Okamoto
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Andrea Fin
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
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30
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Nucleic acid-based fluorescent sensor systems: a review. Polym J 2022. [DOI: 10.1038/s41428-022-00623-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat Chem Biol 2022; 18:191-198. [PMID: 34937911 PMCID: PMC9812287 DOI: 10.1038/s41589-021-00931-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/21/2021] [Indexed: 01/07/2023]
Abstract
Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-Å resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated.
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32
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Chandris P, Giannouli CC, Panayotou G. Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters. Front Cell Dev Biol 2022; 9:725114. [PMID: 35118062 PMCID: PMC8804523 DOI: 10.3389/fcell.2021.725114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of "watching metabolism in real time."
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Affiliation(s)
- Panagiotis Chandris
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
| | | | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
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33
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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34
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Mohamed HI, Gao C, Gui Z, Song Z, Wei D. A novel fluorescent probe with a pyrazolo[4,3- c]quinoline core selectively recognizes c-MYC promoter G-quadruplexes. NEW J CHEM 2022. [DOI: 10.1039/d1nj00098e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer combined with a c-MYC-selective fluorophore could work as the fluorescent core of nucleic acid mimics of fluorescent proteins to locate and image functional biomolecules in cells.
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Affiliation(s)
- Hany I. Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Chao Gao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhikun Gui
- College of Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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35
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Moon JD, Wu J, Dey SK, Litke JL, Li X, Kim H, Jaffrey SR. Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors. Cell Chem Biol 2021; 28:1569-1580.e4. [PMID: 34010626 PMCID: PMC8573057 DOI: 10.1016/j.chembiol.2021.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Small molecules can be imaged in living cells using biosensors composed of RNA. However, RNA-based devices are difficult to design. Here, we describe a versatile platform for designing RNA-based fluorescent small-molecule sensors using naturally occurring highly stable three-way junction RNAs. We show that ligand-binding aptamers and fluorogenic aptamers can be inserted into three-way junctions and connected in a way that enables the three-way junction to function as a small-molecule-regulated fluorescent sensor in vitro and in cells. The sensors are designed so that the interhelical stabilizing interactions in the three-way junction are only induced upon ligand binding. We use these RNA-based devices to measure the dynamics of S-adenosylmethionine levels in mammalian cells in real time. We show that this strategy is compatible with diverse metabolite-binding RNA aptamers, fluorogenic aptamers, and three-way junctions. Overall, these data demonstrate a versatile method for readily generating RNA devices that function in living cells.
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Affiliation(s)
- Jared D Moon
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Jiahui Wu
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Sourav K Dey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Jacob L Litke
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Xing Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Hyaeyeong Kim
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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36
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Huang K, Chen X, Li C, Song Q, Li H, Zhu L, Yang Y, Ren A. Structure-based investigation of fluorogenic Pepper aptamer. Nat Chem Biol 2021; 17:1289-1295. [PMID: 34725509 DOI: 10.1038/s41589-021-00884-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022]
Abstract
Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.
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Affiliation(s)
- Kaiyi Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Huiwen Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, China.
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37
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Fluorescent functional nucleic acid: Principles, properties and applications in bioanalyzing. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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38
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Gu Y, Huang LJ, Zhao W, Zhang TT, Cui MR, Yang XJ, Zhao XL, Chen HY, Xu JJ. Living-Cell MicroRNA Imaging with Self-Assembling Fragments of Fluorescent Protein-Mimic RNA Aptamer. ACS Sens 2021; 6:2339-2347. [PMID: 34028262 DOI: 10.1021/acssensors.1c00453] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As the cellular roles of RNA abundance continue to increase, there is an urgent need for the corresponding tools to elucidate native RNA functions and dynamics, especially those of short, low-abundance RNAs in live cells. Fluorescent RNA aptamers provide a useful strategy to create the RNA tag and biosensor devices. Corn, which binds with 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO), is a good candidate for the RNA tag because of its enhanced photostability and red-shifted spectrum. Herein, we report for the first time the utilization of Corn as a split aptamer system, combined with RNA-initiated fluorescence complementation (RIFC), for monitoring RNA self-assembly and sensing microRNA. In this platform, the 28-nt Corn was divided into two nonfunctional halves (named probe I and probe II), and an additional target RNA recognition and stem part was introduced in each probe. The target RNA can trigger the self-assembly reconstitution of the Corn's G-quadruplex scaffold for DFHO binding and turn-on fluorescence. These probes can be transfected stably into mammalian cells and deliver the light-up fluorescent response to microRNA-21 (miR-21). Significantly, the probes have good photostability, with minimal fluorescence loss after continuous irradiation, and can be used for imaging of miR-21 in living mammalian cells. The proposed method is universal and could be applied to the sensing of other tumor-associated RNAs, including messenger RNA and noncoding RNA, as well as for monitoring RNA/RNA interactions. The Corn-based splitting aptamers show promising potential in the real-time visualization and mechanistic analysis of nucleic acids.
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Affiliation(s)
- Yu Gu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Institute for Materials Science and Engineering, School of Materials Sciences and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Li-Juan Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ting-Ting Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mei-Rong Cui
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue-Jiao Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue-Li Zhao
- College of Chemistry and Molecular Engineering, Zheng-Zhou University, Zhengzhou 450001, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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39
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Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine. Nat Commun 2021; 12:3549. [PMID: 34112799 PMCID: PMC8192780 DOI: 10.1038/s41467-021-23932-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022] Open
Abstract
Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.
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Abstract
Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.
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Affiliation(s)
- Huangmei Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, China.,NYU-ECNU Institute of Physics at NYU Shanghai, Shanghai, China
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41
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Abstract
The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity of their photophysical characterisation, this paper is a model study on Baby Spinach, a truncated Spinach aptamer with half its sequence. Fluorescence and fluorescence excitation spectra of DFHBI complexes of Spinach and Baby Spinach are known to be similar. Surprisingly, a significant divergence between absorption and fluorescence excitation spectra of the DFHBI/RNA complex was observed on conditions of saturation at large excess of RNA over DFHBI. Since absorption spectra were not reported for any Spinach-type aptamer, this effect is new. Quantitative modelling of the absorption spectrum based on competing dark and fluorescent binding sites could explain it. However, following reasoning of fluorescence lifetimes of bound DFHBI, femtosecond-fluorescence lifetime profiles would be more supportive of the notion that the abnormal absorption spectrum is largely caused by trans-isomers formed within the cis-bound DFHBI/RNA complex. Independent of the origin, the unexpected discrepancy between absorption and fluorescence excitation spectra allows for easily accessed screening and insight into the efficiency of a fluorogenic dye/RNA system.
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42
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Banco MT, Ferré-D'Amaré AR. The emerging structural complexity of G-quadruplex RNAs. RNA (NEW YORK, N.Y.) 2021; 27:390-402. [PMID: 33483368 PMCID: PMC7962482 DOI: 10.1261/rna.078238.120] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated by loop nucleotides). Such a sequence restriction, and the stereochemical constraints inherent to RNA (arising, in particular, from the presence of the 2'-OH), dictate relatively simple RNA G4 structures. Recent crystallographic and solution NMR structure determinations of a number of in vitro selected RNA aptamers have revealed RNA G4 structures of unprecedented complexity. Structures of the Sc1 aptamer that binds an RGG peptide from the Fragile-X mental retardation protein, various fluorescence turn-on aptamers (Corn, Mango, and Spinach), and the spiegelmer that binds the complement protein C5a, in particular, reveal complexity hitherto unsuspected in RNA G4s, including nucleotides in syn conformation, locally inverted strand polarity, and nucleotide quartets that are not all-G. Common to these new structures, the sequences folding into G4s do not conform to the requirement that guanine stacks arise from consecutive (contiguous in sequence) nucleotides. This review highlights how emancipation from this constraint drastically expands the structural possibilities of RNA G-quadruplexes.
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Affiliation(s)
- Michael T Banco
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
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43
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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44
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Abstract
The crystallization and structural determination of large RNAs and their complexes remain major bottlenecks in the mechanistic analysis of cellular and viral RNAs. Here, we describe a protocol that combines postcrystallization dehydration and ion replacement that dramatically improved the diffraction quality of crystals of a large gene-regulatory tRNA-mRNA complex. Through this method, the resolution limit of X-ray data extended from 8.5 to 3.2 Å, enabling structure determination. Although this protocol was developed for a particular RNA complex, the general importance of solvent and counterions in nucleic acid structure may render it generally useful for crystallographic analysis of other RNAs.
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45
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Baulin E, Metelev V, Bogdanov A. Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes. Nucleic Acids Res 2020; 48:8675-8685. [PMID: 32687167 PMCID: PMC7470943 DOI: 10.1093/nar/gkaa610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/25/2022] Open
Abstract
Along with nucleobase pairing, base-base stacking interactions are one of the two main types of strong non-covalent interactions that define the unique secondary and tertiary structure of RNA. In this paper we studied two subfamilies of nucleobase-inserted stacking structures: (i) with any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) with any base wedged into a hydrophobic cavity formed by heterocyclic bases of two nucleotides which are one nucleotide apart in sequence (base-wedged element, BWE, i + 2). We have exploited the growing database of natively folded RNA structures in Protein Data Bank to analyze the distribution and structural role of these motifs in RNA. We found that these structural elements initially found in yeast tRNAPhe are quite widespread among the tertiary structures of various RNAs. These motifs perform diverse roles in RNA 3D structure formation and its maintenance. They contribute to the folding of RNA bulges and loops and participate in long-range interactions of single-stranded stretches within RNA macromolecules. Furthermore, both base-intercalated and base-wedged motifs participate directly or indirectly in the formation of RNA functional centers, which interact with various ligands, antibiotics and proteins.
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Affiliation(s)
- Eugene Baulin
- Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Valeriy Metelev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey Bogdanov
- To whom correspondence should be addressed. Tel: +7 495 9393143; Fax: +7 495 9393181;
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46
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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47
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Aufdembrink LM, Khan P, Gaut NJ, Adamala KP, Engelhart AE. Highly specific, multiplexed isothermal pathogen detection with fluorescent aptamer readout. RNA (NEW YORK, N.Y.) 2020; 26:1283-1290. [PMID: 32482894 PMCID: PMC7430665 DOI: 10.1261/rna.075192.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Isothermal, cell-free, synthetic biology-based approaches to pathogen detection leverage the power of tools available in biological systems, such as highly active polymerases compatible with lyophilization, without the complexity inherent to live-cell systems, of which nucleic acid sequence based amplification (NASBA) is well known. Despite the reduced complexity associated with cell-free systems, side reactions are a common characteristic of these systems. As a result, these systems often exhibit false positives from reactions lacking an amplicon. Here we show that the inclusion of a DNA duplex lacking a promoter and unassociated with the amplicon fully suppresses false positives, enabling a suite of fluorescent aptamers to be used as NASBA tags (Apta-NASBA). Apta-NASBA has a 1 pM detection limit and can provide multiplexed, multicolor fluorescent readout. Furthermore, Apta-NASBA can be performed using a variety of equipment, for example, a fluorescence microplate reader, a qPCR instrument, or an ultra-low-cost Raspberry Pi-based 3D-printed detection platform using a cell phone camera module, compatible with field detection.
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Affiliation(s)
- Lauren M Aufdembrink
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Pavana Khan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nathaniel J Gaut
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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48
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Bai J, Luo Y, Wang X, Li S, Luo M, Yin M, Zuo Y, Li G, Yao J, Yang H, Zhang M, Wei W, Wang M, Wang R, Fan C, Zhao Y. A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering. Nat Commun 2020; 11:3847. [PMID: 32737299 PMCID: PMC7395781 DOI: 10.1038/s41467-020-17497-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 07/02/2020] [Indexed: 02/05/2023] Open
Abstract
Reporter systems are routinely used in plant genetic engineering and functional genomics research. Most such plant reporter systems cause accumulation of foreign proteins. Here, we demonstrate a protein-independent reporter system, 3WJ-4 × Bro, based on a fluorescent RNA aptamer. Via transient expression assays in both Escherichia coli and Nicotiana benthamiana, we show that 3WJ-4 × Bro is suitable for transgene identification and as an mRNA reporter for expression pattern analysis. Following stable transformation in Arabidopsis thaliana, 3WJ-4 × Bro co-segregates and co-expresses with target transcripts and is stably inherited through multiple generations. Further, 3WJ-4 × Bro can be used to visualize virus-mediated RNA delivery in plants. This study demonstrates a protein-independent reporter system that can be used for transgene identification and in vivo dynamic analysis of mRNA.
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Affiliation(s)
- Jiuyuan Bai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yao Luo
- State Key Laboratory and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shi Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mei Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Meng Yin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yuanli Zuo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Guolin Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Junyu Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Hua Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Mingdi Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wei Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Maolin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Rui Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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49
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50
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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