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Gu Y, Bai R, Qiu X, Wang X, Lu S, Li CM, Guo C. In Vivo Imaging MicroRNA with Bright Fluorescent RNA Aptamer Through Target-Mediated Entropy-Driven Toehold Exchange. Anal Chem 2024; 96:7609-7617. [PMID: 38687631 DOI: 10.1021/acs.analchem.4c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
MicroRNAs (miRNAs) play vital roles in biological activities, but their in vivo imaging is still challenging due to the low abundance and the lack of efficient fluorescent tools. RNA aptamers with high affinity and low background emerge for bioimaging yet suffering from low brightness. We introduce a rational design based on target-mediated entropy-driven toehold exchange (EDTE) to induce the release of RNA aptamer and subsequently light up corresponding fluorophore, which achieves selective imaging of miRNAs with good stability in both living cells and tumor-bearing mouse. Through tailoring recognition unit of the EDTE probes, highly sensitive imaging of different miRNAs including miRNA-125b and miRNA-21 is achieved, confirming its universal bioimaging applications. In comparison with the reported "one-to-one" model, the EDTE strategy shows a remarkable 4.6-time improvement in signal/noise ratio for intracellular imaging of the same miRNA. Particularly, it realizes sensitive imaging of miRNA in vivo, providing a promising tool in investigating functions and interactions of disease-associated miRNAs.
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Affiliation(s)
- Yu Gu
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Rui Bai
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Xingchen Qiu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Xuefu Road, Suzhou 215009, P. R. China
| | - Xiaobao Wang
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Shasha Lu
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Chang-Ming Li
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
| | - Chunxian Guo
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou 215009, P. R. China
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Tang AA, Afasizheva A, Cano CT, Plath K, Black D, Franco E. Optimization of RNA Pepper Sensors for the Detection of Arbitrary RNA Targets. ACS Synth Biol 2024; 13:498-508. [PMID: 38295291 DOI: 10.1021/acssynbio.3c00426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The development of fluorescent light-up RNA aptamers (FLAPs) has paved the way for the creation of sensors to track RNA in live cells. A major challenge with FLAP sensors is their brightness and limited signal-to-background ratio both in vivo and in vitro. To address this, we develop sensors using the Pepper aptamer, which exhibits superior brightness and photostability when compared to other FLAPs. The sensors are designed to fold into a low fluorescence conformation and to switch to a high fluorescence conformation through toehold or loop-mediated interactions with their RNA target. Our sensors detect RNA targets as short as 20 nucleotides in length with a wide dynamic range over 300-fold in vitro, and we describe strategies for optimizing the sensor's performance for any given RNA target. To demonstrate the versatility of our design approach, we generated Pepper sensors for a range of specific, biologically relevant RNA sequences. Our design and optimization strategies are portable to other FLAPs and offer a promising foundation for future development of RNA sensors with high specificity and sensitivity for detecting RNA biomarkers with multiple applications.
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Affiliation(s)
- Anli A Tang
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Kathrin Plath
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Douglas Black
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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Yan Z, Tang AA, Eshed A, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.02.23290873. [PMID: 37333364 PMCID: PMC10275000 DOI: 10.1101/2023.06.02.23290873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. Here, we describe a class of aptamer-based RNA switches called aptaswitches that recognize specific target nucleic acid molecules and respond by initiating folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide a fast and intense fluorescent readout, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. We demonstrate that aptaswitches can be used to regulate folding of six different fluorescent aptamer/fluorogen pairs, providing a general means of controlling aptamer activity and an array of different reporter colors for multiplexing. By coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed one-pot reactions against RNA extracted from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that can be readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Zackary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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