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Ito K, Tayama T, Uemura S, Iizuka R. Isolation of novel fluorogenic RNA aptamers via in vitro compartmentalization using microbead-display libraries. Talanta 2024; 278:126488. [PMID: 38955098 DOI: 10.1016/j.talanta.2024.126488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/12/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
Fluorogenic RNA aptamers, which specifically bind to fluorogens and dramatically enhance their fluorescence, are valuable for imaging and detecting RNAs and metabolites in living cells. Most fluorogenic RNA aptamers have been identified and engineered through iterative rounds of in vitro selection based on their binding to target fluorogens. While such selection is an efficient approach for generating RNA aptamers, it is less efficient for isolating fluorogenic aptamers because it does not directly screen for fluorogenic properties. In this study, we combined a fluorescence-based in vitro selection technique using water-in-oil microdroplets with an affinity-based selection technique to obtain fluorogenic RNA aptamers. This approach allowed us to identify novel fluorogenic aptamers for a biotin-modified thiazole orange derivative. Our results demonstrate that our approach can expand the diversity of fluorogenic RNA aptamers, thus leading to new applications for the imaging and detection of biomolecules.
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Affiliation(s)
- Keisuke Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomotaka Tayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075, Japan.
| | - Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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2
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Lu X, Passalacqua LFM, Nodwell M, Kong KYS, Caballero-García G, Dolgosheina EV, Ferré-D'Amaré AR, Britton R, Unrau PJ. Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD. Nucleic Acids Res 2024:gkae493. [PMID: 38945550 DOI: 10.1093/nar/gkae493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/21/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024] Open
Abstract
Fluorogenic RNA aptamer tags with high affinity enable RNA purification and imaging. The G-quadruplex (G4) based Mango (M) series of aptamers were selected to bind a thiazole orange based (TO1-Biotin) ligand. Using a chemical biology and reselection approach, we have produced a MII.2 aptamer-ligand complex with a remarkable set of properties: Its unprecedented KD of 45 pM, formaldehyde resistance (8% v/v), temperature stability and ligand photo-recycling properties are all unusual to find simultaneously within a small RNA tag. Crystal structures demonstrate how MII.2, which differs from MII by a single A23U mutation, and modification of the TO1-Biotin ligand to TO1-6A-Biotin achieves these results. MII binds TO1-Biotin heterogeneously via a G4 surface that is surrounded by a stadium of five adenosines. Breaking this pseudo-rotational symmetry results in a highly cooperative and homogeneous ligand binding pocket: A22 of the G4 stadium stacks on the G4 binding surface while the TO1-6A-Biotin ligand completely fills the remaining three quadrants of the G4 ligand binding face. Similar optimization attempts with MIII.1, which already binds TO1-Biotin in a homogeneous manner, did not produce such marked improvements. We use the novel features of the MII.2 complex to demonstrate a powerful optically-based RNA purification system.
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Affiliation(s)
- Xiaocen Lu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Luiz F M Passalacqua
- Laboratory of Nucleic Acids, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Matthew Nodwell
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kristen Y S Kong
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | | | - Elena V Dolgosheina
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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3
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Bartle L, Wellinger RJ. Methods that shaped telomerase research. Biogerontology 2024; 25:249-263. [PMID: 37903970 PMCID: PMC10998806 DOI: 10.1007/s10522-023-10073-8] [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: 08/08/2023] [Accepted: 09/30/2023] [Indexed: 11/01/2023]
Abstract
Telomerase, the ribonucleoprotein (RNP) responsible for telomere maintenance, has a complex life. Complex in that it is made of multiple proteins and an RNA, and complex because it undergoes many changes, and passes through different cell compartments. As such, many methods have been developed to discover telomerase components, delve deep into understanding its structure and function and to figure out how telomerase biology ultimately relates to human health and disease. While some old gold-standard methods are still key for determining telomere length and measuring telomerase activity, new technologies are providing promising new ways to gain detailed information that we have never had access to before. Therefore, we thought it timely to briefly review the methods that have revealed information about the telomerase RNP and outline some of the remaining questions that could be answered using new methodology.
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Affiliation(s)
- Louise Bartle
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavilion, 3201 rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavilion, 3201 rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada.
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4
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Abdolahzadeh A, Ang QR, Caine JR, Panchapakesan SSS, Thio S, Cojocaru R, Unrau PJ. Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection. RNA (NEW YORK, N.Y.) 2024; 30:392-403. [PMID: 38282417 PMCID: PMC10946430 DOI: 10.1261/rna.079833.123] [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: 09/11/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types of light-up RNA Mango Beacons based on a minimized Mango core that induces fluorescence upon binding to a target RNA strand. Our first design is bimolecular in nature and uses a DNA inhibition strand to prevent folding of the Mango aptamer core until binding to a target RNA. Our second design is unimolecular in nature, and features hybridization arms flanking the core that inhibit G-quadruplex folding until refolding is triggered by binding to a target RNA strand. Our third design builds upon this structure, and incorporates a self-inhibiting domain into one of the flanking arms that deliberately binds to, and precludes folding of, the aptamer core until a target is bound. This design separates G-quadruplex folding inhibition and RNA target hybridization into separate modules, enabling a more universal unimolecular beacon design. All three Mango Beacons feature high contrasts and low costs when compared to conventional molecular beacons, with excellent potential for in vitro and in vivo applications.
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Affiliation(s)
- Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Quiana R Ang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Jana R Caine
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | | | - Shinta Thio
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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5
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Sarfraz N, Shafik LK, Stickelman ZR, Shankar U, Moscoso E, Braselmann E. Evaluating Riboglow-FLIM probes for RNA sensing. RSC Chem Biol 2024; 5:109-116. [PMID: 38333191 PMCID: PMC10849122 DOI: 10.1039/d3cb00197k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024] Open
Abstract
We recently developed Riboglow-FLIM, where we genetically tag and track RNA molecules in live cells through measuring the fluorescence lifetime of a small molecule probe that binds the RNA tag. Here, we systematically and quantitatively evaluated key elements of Riboglow-FLIM that may serve as the foundation for Riboglow-FLIM applications and further tool development efforts. Our investigation focused on measuring changes in fluorescence lifetime of representative Riboglow-FLIM probes with different linkers and fluorophores in different environments. In vitro measurements revealed distinct lifetime differences among the probe variants as a result of different linker designs and fluorophore selections. To expand on the platform's versatility, probes in a wide variety of mammalian cell types were examined using fluorescence lifetime imaging microscopy (FLIM), and possible effects on cell physiology were evaluated by metabolomics. The results demonstrated that variations in lifetime were dependent on both probe and cell type. Interestingly, distinct differences in lifetime values were observed between cell lines, while no overall change in cell health was measured. These findings underscore the importance of probe selection and cellular environment when employing Riboglow-FLIM for RNA detection, serving as a foundation for future tool development and applications across diverse fields and biological systems.
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Affiliation(s)
- Nadia Sarfraz
- Department of Chemistry, Georgetown University Washington District of Columbia USA
| | - Luke K Shafik
- Department of Chemistry, Georgetown University Washington District of Columbia USA
| | - Zachary R Stickelman
- Department of Chemistry, Georgetown University Washington District of Columbia USA
| | - Uma Shankar
- Department of Chemistry, Georgetown University Washington District of Columbia USA
| | - Emilia Moscoso
- Department of Chemistry, Georgetown University Washington District of Columbia USA
| | - Esther Braselmann
- Department of Chemistry, Georgetown University Washington District of Columbia USA
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6
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Fischermeier D, Steinmetzger C, Höbartner C, Mitrić R. Conformational preferences of modified nucleobases in RNA aptamers and their effect on Förster resonant energy transfer. Phys Chem Chem Phys 2023; 26:241-248. [PMID: 38054366 DOI: 10.1039/d3cp04704k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Förster resonant energy transfer (FRET) can be utilized in the study of tertiary structures of RNA aptamers, which bind specific fluorophoric ligands to form a fluorogenic aptamer complex. By introducing the emissive nucleobase analog 4-cyanoindole into the fluorogenic Chili RNA aptamer a FRET pair was established. The interpretation of studies aiming to investigate those tertiary structures using FRET, however, relies on prior knowledge about conformational properties of the nucleobase, which govern exciton transfer capabilities. Herein we employed classical molecular dynamics combined with Förster exciton theory to elucidate the preferred orientation relative to proximate bases and the influence on exciton transfer efficiency in multiple substitution sites. We did this by comparing the chromophoric distances emergent from MD simulations with experimental FRET data based on structural data of the native aptamer. We present the outlined methodology as a means to reliably evaluate future nucleobase analogue candidates in terms of their structural behavior and emergent exciton transfer properties as exemplified in the study of the preferred orientation of 4-cyanoindole in the Chili RNA aptamer.
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Affiliation(s)
- David Fischermeier
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Christian Steinmetzger
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Claudia Höbartner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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7
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Eichenberger BT, Griesbach E, Mitchell J, Chao JA. Following the Birth, Life, and Death of mRNAs in Single Cells. Annu Rev Cell Dev Biol 2023; 39:253-275. [PMID: 37843928 DOI: 10.1146/annurev-cellbio-022723-024045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Recent advances in single-molecule imaging of mRNAs in fixed and living cells have enabled the lives of mRNAs to be studied with unprecedented spatial and temporal detail. These approaches have moved beyond simply being able to observe specific events and have begun to allow an understanding of how regulation is coupled between steps in the mRNA life cycle. Additionally, these methodologies are now being applied in multicellular systems and animals to provide more nuanced insights into the physiological regulation of RNA metabolism.
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Affiliation(s)
- Bastian T Eichenberger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
- University of Basel, Basel, Switzerland
| | - Esther Griesbach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
| | - Jessica Mitchell
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
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8
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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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9
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Le P, Ahmed N, Yeo GW. Illuminating RNA biology through imaging. Nat Cell Biol 2022; 24:815-824. [PMID: 35697782 PMCID: PMC11132331 DOI: 10.1038/s41556-022-00933-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/06/2022] [Indexed: 12/14/2022]
Abstract
RNA processing plays a central role in accurately transmitting genetic information into functional RNA and protein regulators. To fully appreciate the RNA life-cycle, tools to observe RNA with high spatial and temporal resolution are critical. Here we review recent advances in RNA imaging and highlight how they will propel the field of RNA biology. We discuss current trends in RNA imaging and their potential to elucidate unanswered questions in RNA biology.
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Affiliation(s)
- Phuong Le
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Noorsher Ahmed
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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