1
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Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589009. [PMID: 38645201 PMCID: PMC11030352 DOI: 10.1101/2024.04.11.589009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.
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Affiliation(s)
- Maxim Oleynikov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
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2
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Song Q, Tai X, Ren Q, Ren A. Structure-based insights into fluorogenic RNA aptamers. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39148467 DOI: 10.3724/abbs.2024142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024] Open
Abstract
Fluorogenic RNA aptamers are in vitro-selected RNA molecules capable of binding to specific fluorophores, significantly increasing their intrinsic fluorescence. Over the past decade, the color palette of fluorescent RNA aptamers has greatly expanded. The emergence and development of these fluorogenic RNA aptamers has introduced a powerful approach for visualizing RNA localization and transport with high spatiotemporal resolution in live cells. To date, a variety of tertiary structures of fluorogenic RNA aptamers have been determined using X-ray crystallography or NMR spectroscopy. Many of these fluorogenic RNA aptamers feature base quadruples or base triples in their fluorophore-binding sites. This review summarizes the structure-based investigations of fluorogenic RNA aptamers, with a focus on their overall folds, ligand-binding pockets and fluorescence activation mechanisms. Additionally, the exploration of how structures guide rational optimization to enhance RNA visualization techniques is discussed.
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Affiliation(s)
- Qianqian Song
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiaoqing Tai
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Qianyu Ren
- Agricultural College, Yangzhou University, Yangzhou 225009, China
| | - Aiming Ren
- Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
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3
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DasGupta S. Synthetic antibodies for accelerated RNA crystallography. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1869. [PMID: 39187256 DOI: 10.1002/wrna.1869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/04/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024]
Abstract
RNA structure is crucial to a wide range of cellular processes. The intimate relationship between macromolecular structure and function necessitates the determination of high-resolution structures of functional RNA molecules. X-ray crystallography is the predominant technique used for macromolecular structure determination; however, solving RNA structures has been more challenging than their protein counterparts, as reflected in their poor representation in the Protein Data Bank (<1%). Antibody-assisted RNA crystallography is a relatively new technique that promises to accelerate RNA structure determination by employing synthetic antibodies (Fabs) as crystallization chaperones that are specifically raised against target RNAs. Antibody chaperones facilitate the formation of ordered crystal lattices by minimizing RNA flexibility and replacing unfavorable RNA-RNA contacts with contacts between chaperone molecules. Atomic coordinates of these antibody fragments can also be used as search models to obtain phase information during structure determination. Antibody-assisted RNA crystallography has enabled the structure determination of 15 unique RNA targets, including 11 in the last 6 years. In this review, I cover the historical development of antibody fragments as crystallization chaperones and their application to diverse RNA targets. I discuss how the first structures of antibody-RNA complexes informed the design of second-generation antibodies and led to the development of portable crystallization modules that have greatly reduced the uncertainties associated with RNA crystallography. Finally, I outline unexplored avenues that can increase the impact of this technology in structural biology research and discuss potential applications of antibodies as affinity reagents for interrogating RNA biology outside of their use in crystallography. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
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4
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Terrell JR, Le TT, Paul A, Brinton MA, Wilson WD, Poon GMK, Germann MW, Siemer JL. Structure of an RNA G-quadruplex from the West Nile virus genome. Nat Commun 2024; 15:5428. [PMID: 38926367 PMCID: PMC11208454 DOI: 10.1038/s41467-024-49761-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains arthropod-transmitted, positive-sense, single-stranded RNA viruses that cause significant human disease globally. Computational studies have identified multiple potential G-quadruplex sites that are conserved across members of this genus. Subsequent biophysical studies established that some G-quadruplexes predicted in Zika and tickborne encephalitis virus genomes can form and known quadruplex binders reduced viral yields from cells infected with these viruses. The susceptibility of RNA to degradation and the variability of loop regions have made structure determination challenging. Despite these difficulties, we report a high-resolution structure of the NS5-B quadruplex from the West Nile virus genome. Analysis reveals two stacked tetrads that are further stabilized by a stacked triad and transient noncanonical base pairing. This structure expands the landscape of solved RNA quadruplex structures and demonstrates the diversity and complexity of biological quadruplexes. We anticipate that the availability of this structure will assist in solving further viral RNA quadruplexes and provides a model for a conserved antiviral target in Orthoflavivirus genomes.
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Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Thao T Le
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jessica L Siemer
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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5
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Zhang C, Dang W, Zhang J, Wang C, Zhong P, Wang Z, Yang Y, Wang Y, Yan X. Development of a paper-based transcription aptasensor for convenient urinary uric acid self-testing. Int J Biol Macromol 2024; 271:132241. [PMID: 38768916 DOI: 10.1016/j.ijbiomac.2024.132241] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
The abnormal uric acid (UA) level in urine can serve as warning signals of many diseases, such as gout and metabolic cardiovascular diseases. The current methods for detecting UA face limitations of instrument dependence and the requirement for non-invasiveness, making it challenging to fulfill the need for home-based application. In this study, we designed an aptasensor that combined UA-specific transcriptional regulation and a fluorescent RNA aptamer for convenient urinary UA testing. The concentration of UA can be translated into the intensity of fluorescent signals. The aptasensor showed higher sensitivity and more robust anti-interference performance. UA levels in the urine of different volunteers could be accurately tested using this method. In addition, a paper-based aptasensor for UA self-testing was manufactured, in which the urinary UA levels could be determined using a smartphone-based colorimetric approach. This work not only demonstrates a new approach for the design of disease-associated aptasensor, but also offers promising ideas for home-based detection of UA.
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Affiliation(s)
- Chengyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Weifan Dang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingjing Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Cong Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Peng Zhong
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhaoxin Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yufan Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuefei Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Xiaohui Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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6
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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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7
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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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8
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Vianney YM, Jana J, Weisz K. A pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid. Chemistry 2024; 30:e202400722. [PMID: 38497675 DOI: 10.1002/chem.202400722] [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: 02/22/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/19/2024]
Abstract
A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs. NMR-derived high-resolution structures reveal that an adenine protonation is prerequisite for the formation of a non-canonical base quartet, capping the outer G-tetrad at the quadruplex-duplex interface and stabilizing the antiparallel chair conformation in an acidic environment. Being directly associated with interactions at the quadruplex-duplex interface, this unique pH-dependent topological transition is fully reversible. Coupled with a conformation-sensitive optical readout demonstrated as a proof of concept using the fluorescent dye thiazole orange, the present quadruplex-duplex hybrid architecture represents a potentially valuable pH-sensing system responsive in a physiological pH range of 7±1.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489, Greifswald, Germany
| | - Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489, Greifswald, Germany
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9
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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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10
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Mumbleau M, Chevance F, Hughes K, Hammond MC. Investigating the Effect of RNA Scaffolds on the Multicolor Fluorogenic Aptamer Pepper in Different Bacterial Species. ACS Synth Biol 2024; 13:1093-1099. [PMID: 38593047 PMCID: PMC11037261 DOI: 10.1021/acssynbio.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024]
Abstract
RNA synthetic biology tools have primarily been applied in E. coli; however, many other bacteria are of industrial and clinical significance. Thus, the multicolor fluorogenic aptamer Pepper was evaluated in both Gram-positive and Gram-negative bacteria. Suitable HBC-Pepper dye pairs were identified that give blue, green, or red fluorescence signals in the E. coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium (S. Typhimurium). Furthermore, we found that different RNA scaffolds have a drastic effect on in vivo fluorescence, which did not correlate with the in vitro folding efficiency. One such scaffold termed DF30-tRNA displays 199-fold greater fluorescence than the Pepper aptamer alone and permits simultaneous dual color imaging in live cells.
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Affiliation(s)
- Madeline
M. Mumbleau
- Department
of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Fabienne Chevance
- School
of Biological Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Kelly Hughes
- School
of Biological Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ming C. Hammond
- Department
of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
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11
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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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12
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Aggarwal T, Wang L, Gutierrez B, Guven H, Erguven H, Izgu EC. A Small-Molecule Approach to Bypass In Vitro Selection of New Aptamers: Designer Pre-Ligands Turn Baby Spinach into Sensors for Reactive Inorganic Targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.29.551132. [PMID: 38168427 PMCID: PMC10760011 DOI: 10.1101/2023.07.29.551132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Fluorescent light-up aptamer (FLAP) systems are promising biosensing platforms that can be genetically encoded. Here, we describe how a single FLAP that works with specific organic ligands can detect multiple, structurally unique, non-fluorogenic, and reactive inorganic targets. We developed 4-O-functionalized benzylidene imidazolinones as pre-ligands with suppressed fluorescent binding interactions with the RNA aptamer Baby Spinach. Inorganic targets, hydrogen sulfide (H2S) or hydrogen peroxide (H2O2), can specifically convert these pre-ligands into the native benzylidene imidazolinones, and thus be detected with Baby Spinach. Adaptation of this approach to live cells opened a new opportunity for top-down construction of whole-cell sensors: Escherichia coli transformed with a Baby Spinach-encoding plasmid and incubated with pre-ligands generated fluorescence in response to exogenous H2S or H2O2. Our approach eliminates the requirement of in vitro selection of a new aptamer sequence for molecular target detection, allows for the detection of short-lived targets, thereby advancing FLAP systems beyond their current capabilities. Leveraging the functional group reactivity of small molecules can lead to cell-based sensors for inorganic molecular targets, exploiting a new synergism between synthetic organic chemistry and synthetic biology.
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Affiliation(s)
- Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Liming Wang
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Bryan Gutierrez
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Hakan Guven
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Huseyin Erguven
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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13
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Rocca R, Grillone K, Citriniti EL, Gualtieri G, Artese A, Tagliaferri P, Tassone P, Alcaro S. Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches. Eur J Med Chem 2023; 261:115850. [PMID: 37839343 DOI: 10.1016/j.ejmech.2023.115850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The growing information currently available on the central role of non-coding RNAs (ncRNAs) including microRNAs (miRNAS) and long non-coding RNAs (lncRNAs) for chronic and degenerative human diseases makes them attractive therapeutic targets. RNAs carry out different functional roles in human biology and are deeply deregulated in several diseases. So far, different attempts to therapeutically target the 3D RNA structures with small molecules have been reported. In this scenario, the development of computational tools suitable for describing RNA structures and their potential interactions with small molecules is gaining more and more interest. Here, we describe the most suitable strategies to study ncRNAs through computational tools. We focus on methods capable of predicting 2D and 3D ncRNA structures. Furthermore, we describe computational tools to identify, design and optimize small molecule ncRNA binders. This review aims to outline the state of the art and perspectives of computational methods for ncRNAs over the past decade.
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Affiliation(s)
- Roberta Rocca
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | | | - Anna Artese
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy.
| | | | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
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14
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Dan Q, Jiang X, Wang R, Dai Z, Sun D. Biogenic Imaging Contrast Agents. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207090. [PMID: 37401173 PMCID: PMC10477908 DOI: 10.1002/advs.202207090] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/08/2023] [Indexed: 07/05/2023]
Abstract
Imaging contrast agents are widely investigated in preclinical and clinical studies, among which biogenic imaging contrast agents (BICAs) are developing rapidly and playing an increasingly important role in biomedical research ranging from subcellular level to individual level. The unique properties of BICAs, including expression by cells as reporters and specific genetic modification, facilitate various in vitro and in vivo studies, such as quantification of gene expression, observation of protein interactions, visualization of cellular proliferation, monitoring of metabolism, and detection of dysfunctions. Furthermore, in human body, BICAs are remarkably helpful for disease diagnosis when the dysregulation of these agents occurs and can be detected through imaging techniques. There are various BICAs matched with a set of imaging techniques, including fluorescent proteins for fluorescence imaging, gas vesicles for ultrasound imaging, and ferritin for magnetic resonance imaging. In addition, bimodal and multimodal imaging can be realized through combining the functions of different BICAs, which helps overcome the limitations of monomodal imaging. In this review, the focus is on the properties, mechanisms, applications, and future directions of BICAs.
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Affiliation(s)
- Qing Dan
- Shenzhen Key Laboratory for Drug Addiction and Medication SafetyDepartment of UltrasoundInstitute of Ultrasonic MedicinePeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhen518036P. R. China
| | - Xinpeng Jiang
- Department of Biomedical EngineeringCollege of Future TechnologyPeking UniversityBeijing100871P. R. China
| | - Run Wang
- Shenzhen Key Laboratory for Drug Addiction and Medication SafetyDepartment of UltrasoundInstitute of Ultrasonic MedicinePeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhen518036P. R. China
| | - Zhifei Dai
- Department of Biomedical EngineeringCollege of Future TechnologyPeking UniversityBeijing100871P. R. China
| | - Desheng Sun
- Shenzhen Key Laboratory for Drug Addiction and Medication SafetyDepartment of UltrasoundInstitute of Ultrasonic MedicinePeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhen518036P. R. China
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15
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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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16
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Bains J, Qureshi N, Ceylan B, Wacker A, Schwalbe H. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function. Nucleic Acids Res 2023; 51:e82. [PMID: 37409574 PMCID: PMC10450168 DOI: 10.1093/nar/gkad574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Cell-free protein synthesis assays have become a valuable tool to understand transcriptional and translational processes. Here, we established a fluorescence-based coupled in vitro transcription-translation assay as a read-out system to simultaneously quantify mRNA and protein levels. We utilized the well-established quantification of the expression of shifted green fluorescent protein (sGFP) as a read-out of protein levels. In addition, we determined mRNA quantities using a fluorogenic Mango-(IV) RNA aptamer that becomes fluorescent upon binding to the fluorophore thiazole orange (TO). We utilized a Mango-(IV) RNA aptamer system comprising four subsequent Mango-(IV) RNA aptamer elements with improved sensitivity by building Mango arrays. The design of this reporter assay resulted in a sensitive read-out with a high signal-to-noise ratio, allowing us to monitor transcription and translation time courses in cell-free assays with continuous monitoring of fluorescence changes as well as snapshots of the reaction. Furthermore, we applied this dual read-out assay to investigate the function of thiamine-sensing riboswitches thiM and thiC from Escherichia coli and the adenine-sensing riboswitch ASW from Vibrio vulnificus and pbuE from Bacillus subtilis, which represent transcriptional and translational on- and off-riboswitches, respectively. This approach enabled a microplate-based application, a valuable addition to the toolbox for high-throughput screening of riboswitch function.
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Affiliation(s)
- Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
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17
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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18
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Dalmau D, Crespo O, Matxain JM, Urriolabeitia EP. Fluorescence Amplification of Unsaturated Oxazolones Using Palladium: Photophysical and Computational Studies. Inorg Chem 2023. [PMID: 37315074 DOI: 10.1021/acs.inorgchem.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Weakly fluorescent (Z)-4-arylidene-5-(4H)-oxazolones (1), ΦPL < 0.1%, containing a variety of conjugated aromatic fragments and/or charged arylidene moieties, have been orthopalladated by reaction with Pd(OAc)2. The resulting dinuclear complexes (2) have the oxazolone ligands bonded as a C^N-chelate, restricting intramolecular motions involving the oxazolone. From 2, a variety of mononuclear derivatives, such as [Pd(C^N-oxazolone)(O2CCF3)(py)] (3), [Pd(C^N-oxazolone)(py)2](ClO4) (4), [Pd(C^N-oxazolone)(Cl)(py)] (5), and [Pd(C^N-oxazolone)(X)(NHC)] (6, 7), have been prepared and fully characterized. Most of complexes 3-6 are strongly fluorescent in solution in the range of wavelengths from green to yellow, with values of ΦPL up to 28% (4h), which are among the highest values of quantum yield ever reported for organometallic Pd complexes with bidentate ligands. This means that the introduction of the Pd in the oxazolone scaffold produces in some cases an amplification of the fluorescence of several orders of magnitude from the free ligand 1 to complexes 3-6. Systematic variations of the substituents of the oxazolones and the ancillary ligands show that the wavelength of emission is tuned by the nature of the oxazolone, while the quantum yield is deeply influenced by the change of ligands. TD-DFT studies of complexes 3-6 show a direct correlation between the participation of the Pd orbitals in the HOMO and the loss of emission through non-radiative pathways. This model allows the understanding of the amplification of the fluorescence and the future rational design of new organopalladium systems with improved properties.
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Affiliation(s)
- David Dalmau
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Olga Crespo
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Jon M Matxain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU and Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Euskadi, Spain
| | - Esteban P Urriolabeitia
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
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19
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Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR, Ferré-D'Amaré AR. Intricate 3D architecture of a DNA mimic of GFP. Nature 2023; 618:1078-1084. [PMID: 37344591 PMCID: PMC10754392 DOI: 10.1038/s41586-023-06229-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.
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Affiliation(s)
- Luiz F M Passalacqua
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael T Banco
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jared D Moon
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Xing Li
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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20
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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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21
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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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22
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Ke HW, Sung K. 7-membered-ring effect on fluorescence quantum yield: does metal-complexation-induced twisting-inhibition of an amino GFP chromophore derivative enhance fluorescence? Phys Chem Chem Phys 2023; 25:14627-14634. [PMID: 37194347 DOI: 10.1039/d3cp00467h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To investigate two aspects, namely, (1) the 7-membered-ring effect on fluorescence quantum yield and (2) whether metal-complexation-induced twisting-inhibition of an amino green fluorescent protein (GFP) chromophore derivative is bound to enhance fluorescence, a novel GFP-chromophore-based triamine ligand, (Z)-o-PABDI, is designed and synthesized. Before complexation with metal ions, the S1 excited state of (Z)-o-PABDI undergoes τ-torsion relaxation (Z/E photoisomerization) with a Z/E photoisomerization quantum yield of 0.28, forming both ground-state (Z)- and (E)-o-PABDI isomers. Since (E)-o-PABDI is less stable than (Z)-o-PABDI, it is thermo-isomerized back to (Z)-o-PABDI at room temperature in acetonitrile with a first-order rate constant of (1.366 ± 0.082) × 10-6 s-1. After complexation with a Zn2+ ion, (Z)-o-PABDI as a tridentate ligand forms a 1 : 1 complex with the Zn2+ ion in acetonitrile and in the solid state, resulting in complete inhibition of the φ-torsion and τ-torsion relaxations, which does not enhance fluorescence but causes fluorescence quenching. (Z)-o-PABDI also forms complexes with other first-row transition metal ions Mn2+, Fe3+, Co2+, Ni2+ and Cu2+, generating almost the same fluorescence quenching effect. By comparison with the 2/Zn2+ complex, in which a 6-membered ring of Zn2+-complexation enhances fluorescence significantly (a positive 6-membered-ring effect on fluorescence quantum yield), we find that the flexible 7-membered rings of the (Z)-o-PABDI/Mn+ complexes trigger their S1 excited states to relax through internal conversion at a rate much faster than fluorescence (a negative 7-membered-ring effect on fluorescence quantum yield), leading to fluorescence quenching regardless of the type of transition metal that complexes with (Z)-o-PABDI.
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Affiliation(s)
- Hao-Wei Ke
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
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23
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Torelli E, Shirt-Ediss B, Navarro SA, Manzano M, Vizzini P, Krasnogor N. Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing. Int J Mol Sci 2023; 24:ijms24108483. [PMID: 37239830 DOI: 10.3390/ijms24108483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system is assembled in an E. coli-based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a 'bio-orthogonal' hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect the femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include the real-time monitoring of the self-assembly of nucleic-acid-based devices in vivo and of the intracellular delivery of therapeutic nanostructures, as well as the in vitro and in vivo detection of different DNA/RNA targets.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Ben Shirt-Ediss
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Silvia A Navarro
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, 33100 Udine, Italy
| | - Priya Vizzini
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, 33100 Udine, Italy
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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24
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Serine 970 of RNA helicase MOV10 is phosphorylated and controls unfolding activity and fate of mRNAs targeted for AGO2-mediated silencing. J Biol Chem 2023; 299:104577. [PMID: 36871759 PMCID: PMC10070924 DOI: 10.1016/j.jbc.2023.104577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/07/2023] Open
Abstract
MOV10 is an RNA helicase that is required for organismal development and is highly expressed in postnatal brain. MOV10 was identified as an AGO2 associated protein that is also necessary for AGO2-mediated silencing. AGO2 is the primary effector of the miRNA pathway. MOV10 has been shown to be ubiquitinated, leading to its degradation and release from bound mRNAs but no other post-translational modifications with functional implications have been described. Using mass spectrometry, we show that MOV10 is phosphorylated in cells at the C-terminus, specifically at serine 970 (S970). Substitution of S970 to phospho-mimic aspartic acid (S970D) blocked unfolding of an RNA G-quadruplex, similar to when the helicase domain was mutated (K531A). In contrast, the alanine substitution (S970A) of MOV10 unfolded the model RNA G-quadruplex. To examine its role in cells, our RNA-seq analysis showed that the expression of S970D causes decreased expression of MOV10 enhanced Cross-Linking Immunoprecipitation (eCLIP) targets compared to WT. Introduction of S970A had an intermediate effect, suggesting that S970 was protective of mRNAs. In whole cell extracts, MOV10 and its substitutions bound AGO2 comparably; however, knockdown of AGO2 abrogated the S970D-induced mRNA degradation. Thus, MOV10 activity protects mRNA from AGO2; phosphorylation of S970 restricts this activity resulting in AGO2-mediated mRNA degradation. S970 is positioned C-terminal to the defined MOV10-AGO2 interaction site and is proximal to a disordered region that likely modulates AGO2 interaction with target mRNAs upon phosphorylation. In summary, we provide evidence for a model whereby MOV10 phosphorylation facilitates AGO2 association with the 3'UTR of translating mRNAs that leads to their degradation.
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25
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Jansson-Fritzberg LI, Sousa CI, Smallegan MJ, Song JJ, Gooding AR, Kasinath V, Rinn JL, Cech TR. DNMT1 inhibition by pUG-fold quadruplex RNA. RNA (NEW YORK, N.Y.) 2023; 29:346-360. [PMID: 36574982 PMCID: PMC9945446 DOI: 10.1261/rna.079479.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Aberrant DNA methylation is one of the earliest hallmarks of cancer. DNMT1 is responsible for methylating newly replicated DNA, but the precise regulation of DNMT1 to ensure faithful DNA methylation remains poorly understood. A link between RNA and chromatin-associated proteins has recently emerged, and several studies have shown that DNMT1 can be regulated by a variety of RNAs. In this study, we have confirmed that human DNMT1 indeed interacts with multiple RNAs, including its own nuclear mRNA. Unexpectedly, we found that DNMT1 exhibits a strong and specific affinity for GU-rich RNAs that form a pUG-fold, a noncanonical G-quadruplex. We find that pUG-fold-capable RNAs inhibit DNMT1 activity by inhibiting binding of hemimethylated DNA, and we additionally provide evidence for multiple RNA binding modes with DNMT1. Together, our data indicate that a human chromatin-associated protein binds to and is regulated by pUG-fold RNA.
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Affiliation(s)
- Linnea I Jansson-Fritzberg
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Camila I Sousa
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Michael J Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Jessica J Song
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Anne R Gooding
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Vignesh Kasinath
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - John L Rinn
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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26
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Chen W, Zhao X, Yang N, Li X. Single mRNA Imaging with Fluorogenic RNA Aptamers and Small-molecule Fluorophores. Angew Chem Int Ed Engl 2023; 62:e202209813. [PMID: 36420710 DOI: 10.1002/anie.202209813] [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: 07/05/2022] [Revised: 11/07/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Messenger RNA (mRNA) is the fundamental information transfer system in the cell. Tracking single mRNA from transcription to degradation with fluorescent probes provides spatiotemporal information in cells about how the genetic information is transferred from DNA to proteins. The traditional single mRNA imaging approach utilizes RNA hairpins (e.g. MS2) and tethered fluorescent protein as probes. As an exciting alternative, RNA aptamers: small-molecule fluorophores (SFs) systems have emerged as novel single mRNA imaging probes since 2019, exhibiting several advantages including fluorogenic ability and minimal perturbation. This review summarizes all five reported RNA aptamers: SFs systems for single mRNA imaging in living cells so far. It also discusses the challenges and provides prospects for single mRNA imaging applications. This review is expected to inspire researchers to develop RNA aptamers: SFs systems for studying gene expression at single-molecule resolution in cells.
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Affiliation(s)
- Wei Chen
- Institute of Cytology and Genetics, the Hengyang Key Laboratory of Cellular Stress Biology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Beijing Institutes of Life Science, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Science, Beijing, 100101, China
| | - Xiaoying Zhao
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Nanyang Yang
- Institute of Cytology and Genetics, the Hengyang Key Laboratory of Cellular Stress Biology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xing Li
- Beijing Institutes of Life Science, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Science, Beijing, 100101, China
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27
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Endoh T, Tan JH, Chen SB, Sugimoto N. Cladogenetic Orthogonal Light-Up Aptamers for Simultaneous Detection of Multiple Small Molecules in Cells. Anal Chem 2023; 95:976-985. [PMID: 36541622 DOI: 10.1021/acs.analchem.2c03598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent successes in construction of light-up RNA aptamers allowed fluorescence-based live-cell imaging of RNAs. In addition, light-up aptamers have been converted into signaling aptamers that enable fluorometric detection of small chemicals. To date, only a single target chemical has been detected at a time in cells. In this study, we selected cladogenetic orthogonal light-up aptamers that output three different colors from the RNA library having the same ligand binding core. Two of the three functioned in mammalian cells. These two aptamers, which fluoresce blue and green upon binding of cognate fluorogen, were converted into signaling aptamers. Using these signaling aptamers in combination with a previously described light-up aptamer with red fluorescence, we demonstrated simultaneous detection of multiple chemicals in living cells. The cladogenetic orthogonal light-up aptamers developed in this study and the simple strategy for rational designing of the signaling aptamers will provide innovative advances in the field of RNA-based bioimaging.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe650-0047, Japan
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou510006, China
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe650-0047, Japan
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28
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Soni R, Krishna AM, More SH, Sharma A. Reversible Modulation of Aptamer-Ligand Binding in RNA Light-Up Aptamers Containing G-Quadruplex Using Chemical Stimuli. Chembiochem 2023; 24:e202200574. [PMID: 36352557 DOI: 10.1002/cbic.202200574] [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: 10/04/2022] [Revised: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Regulating a system in equilibrium transiently to out-of-equilibrium by using certain stimuli is the strategy used by natural biomolecules to function. Herein, we showed that the interaction of synthetic RNA aptamers, having a G-quadruplex core structure, with their corresponding ligands could be regulated from their equilibrium state to non-equilibrium state in a reversible manner using simple chemical stimuli (Ag+ and cysteine). The approach would be useful for designing aptamer regulators that work in a dynamic nucleic acid network, where a strict control on aptamer-ligand interaction is needed. In addition, to the best of our knowledge, this is the first report which shows that RNA G-quadruplexes can be disrupted by the addition of silver ions. This would be useful not only in designing RNA-based sensors or regulators but would also be useful for understanding the role of metal ions in RNA folding and catalysis.
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Affiliation(s)
- Rashi Soni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - A Murali Krishna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Shahaji H More
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Ashwani Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India.,Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
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29
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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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30
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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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31
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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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32
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Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy. Toxins (Basel) 2022; 14:toxins14090622. [PMID: 36136560 PMCID: PMC9505997 DOI: 10.3390/toxins14090622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures.
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33
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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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34
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and 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
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and 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.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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35
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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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36
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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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37
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Geraci I, Autour A, Pietruschka G, Shiian A, Borisova M, Mayer C, Ryckelynck M, Mayer G. Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells. ACS Chem Biol 2022; 17:1164-1173. [PMID: 35427113 DOI: 10.1021/acschembio.2c00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The visualization of metabolic flux in real time requires sensor molecules that transduce variations of metabolite concentrations into an appropriate output signal. In this regard, fluorogenic RNA-based biosensors are promising molecular tools as they fluoresce only upon binding to another molecule. However, to date no such sensor is available that enables the direct observation of key metabolites in mammalian cells. Toward this direction, we selected and characterized an RNA light-up sensor designed to respond to fructose 1,6-bisphosphate and applied it to probe glycolytic flux variation in mammal cells.
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Affiliation(s)
- Ignazio Geraci
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Alexis Autour
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, 67084 Strasbourg, France
| | - Georg Pietruschka
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Aleksandra Shiian
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, 67084 Strasbourg, France
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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38
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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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39
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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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40
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Hostetter ER, Keyes JR, Poon I, Nguyen JP, Nite JM, Jimenez Hoyos CA, Smith CA. Prediction of Fluorophore Brightness in Designed Mini Fluorescence Activating Proteins. J Chem Theory Comput 2022; 18:3190-3203. [PMID: 35417158 DOI: 10.1021/acs.jctc.1c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The de novo computational design of proteins with predefined three-dimensional structure is becoming much more routine due to advancements both in force fields and algorithms. However, creating designs with functions beyond folding is more challenging. In that regard, the recent design of small beta barrel proteins that activate the fluorescence of an exogenous small molecule chromophore (DFHBI) is noteworthy. These proteins, termed mini fluorescence activating proteins (mFAPs), have been shown to increase the brightness of the chromophore more than 100-fold upon binding to the designed ligand pocket. The design process created a large library of variants with different brightness levels but gave no rational explanation for why one variant was brighter than another. Here, we use quantum mechanics and molecular dynamics simulations to investigate how molecular flexibility in the ground and excited states influences brightness. We show that the ability of the protein to resist dihedral angle rotation of the chromophore is critical for predicting brightness. Our simulations suggest that the mFAP/DFHBI complex has a rough energy landscape, requiring extensive ground-state sampling to achieve converged predictions of excited-state kinetics. While computationally demanding, this roughness suggests that mFAP protein function can be enhanced by reshaping the energy landscape toward conformations that better resist DFHBI bond rotation.
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Affiliation(s)
- Emma R Hostetter
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Jeffrey R Keyes
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Ivy Poon
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Justin P Nguyen
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Jacob M Nite
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | -
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Carlos A Jimenez Hoyos
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, 52 Lawn Ave, Middletown, Connecticut 06459, United States
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41
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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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42
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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43
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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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44
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Harish B, Wang J, Hayden EJ, Grabe B, Hiller W, Winter R, Royer CA. Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation. Biophys J 2022; 121:421-429. [PMID: 34971617 PMCID: PMC8822612 DOI: 10.1016/j.bpj.2021.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.
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Affiliation(s)
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy
| | - Eric J Hayden
- Department of Biology, Boise State University, Boise
| | - Bastian Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy.
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45
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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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46
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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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47
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Liang Y, Miao S, Mao J, Devari S, Gonzalez M, Bong D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry 2022; 28:e202103616. [PMID: 34693570 PMCID: PMC8758549 DOI: 10.1002/chem.202103616] [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: 10/06/2021] [Indexed: 01/12/2023]
Abstract
We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Jie Mao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Maricarmen Gonzalez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
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48
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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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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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50
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Citartan M. The dynamicity of light-up aptamers in one-pot in vitro diagnostic assays. Analyst 2021; 147:10-21. [PMID: 34860215 DOI: 10.1039/d1an01690c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Light-up aptamers are aptamers that ignite the fluorescence emission of certain dyes upon binding. Widely harnessed in in vivo imaging, the binding capacity of the light-up aptamers can also be deployed in in vitro diagnostic assays, engendering a mix-and-read format. Intrigued by this, I intend to provide an overview of the various formats of diagnostic assays developed using light-up aptamers from the direct modulation of the light-up aptamers, split aptamer-based configuration, strand displacement, in vitro transcription-based one-pot diagnostic assay, CRISPR-Cas system to the measurement of the ion reliance. The incorporation of the light-up aptamers into each configuration is expounded and further supported by describing the exemplary assays developed thus far. It is anticipated that the present study can be enlightening to any researchers who aspire to embark on the development of one-pot in vitro diagnostic assays based on light-up aptamers.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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