1
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Wang L, Alkhamis O, Canoura J, Yu H, Xiao Y. Rapid Nuclease-Assisted Selection of High-Affinity Small-Molecule Aptamers. J Am Chem Soc 2024; 146:21296-21307. [PMID: 39042584 DOI: 10.1021/jacs.4c00748] [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: 07/25/2024]
Abstract
Aptamers are nucleic acid bioreceptors that have been widely utilized for a variety of biosensing applications, including in vivo detection methods that would not be possible with antibody-based systems. However, it remains challenging to generate high-quality aptamers for small molecule targets, particularly for use under physiological conditions. We present a highly effective aptamer selection technology for small-molecule targets that utilizes the nuclease EcoRI to remove nonspecific or weakly binding sequences in solution phase, rapidly enriching high-affinity target binders within just a few rounds of selection. As proof-of-concept, we used our nuclease-assisted SELEX (NA-SELEX) method to isolate aptamers for a synthetic cannabinoid, AB-FUBINACA. Within five rounds, we identified two highly specific aptamers that exhibit nanomolar affinity at physiological temperature. We also demonstrate the robustness and reproducibility of NA-SELEX by performing the same selection experiment with fresh reagents and libraries, obtaining the same two aptamers as well as two other high-quality aptamer candidates. Finally, we compare NA-SELEX against a conventional library-immobilized SELEX screen for AB-FUBINACA using the same screening conditions, identifying aptamers with 25-100-fold weaker affinity after 11 rounds of selection. NA-SELEX therefore could be an effective selection method for the isolation of high-quality aptamers for small-molecule targets.
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Affiliation(s)
- Linlin Wang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
| | - Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
| | - Haixiang Yu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
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2
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Zhang Y, Mou Y, Chen M, Lin X, Zhao Y, Luo X. Binary split fluorescent biosensor based on lettuce DNA aptamer for label-free and enzyme-free analysis of hepatitis B viral DNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4561-4569. [PMID: 38912590 DOI: 10.1039/d4ay00713a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Hepatitis B virus (HBV) acts as a severe public health threat, causing chronic liver diseases. Although the quantified evaluation of HBV infection can be obtained by estimating the capacity of the HBV DNA genome, it still lacks an effective and robust detection method without using enzymes or chemical labeling. Herein, we have designed a binary split fluorescent DNA aptasensor (bsFDA) by rationally splitting the lettuce aptamer into two functional DNA short chains and utilizing the HBV DNA segment complementary sequences (HDs). In this strategy, the bsFDA has been investigated to specifically recognize the HDs, forming a triplex DNA with the lettuce aptamer structure. Meanwhile, the turn-on fluorescence of bsFDA is obtained upon formation of a fluorescent complex between DFHO and the triplex DNA structure, allowing the enzyme-free, label-free, fast-responsive, and reliable fluorescence readout for detecting HDs and the potential HDs mutants. Moreover, bsFDA has been applied for spiked HDs analysis in different real matrixes, including human serum and cell lysate. The satisfactory recovery rates and reproducibility of the bsFDA reveal its potential detection efficacy for HDs analysis in biological samples. Overall, bsFDA holds great potential in developing functionalized aptasensors and realizing viral genome analysis in biological research.
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Affiliation(s)
- Yanfei Zhang
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Yue Mou
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Meiyun Chen
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Xinru Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Yujie Zhao
- Medical College, Guangxi University, Nanning 530004, P. R. China.
| | - Xingyu Luo
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
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3
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Kuo YA, Chen YI, Wang Y, Korkmaz Z, Yonas S, He Y, Nguyen TD, Hong S, Nguyen AT, Kim S, Seifi S, Fan PH, Wu Y, Yang Z, Liu HW, Lu Y, Ren P, Yeh HC. Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602435. [PMID: 39026723 PMCID: PMC11257435 DOI: 10.1101/2024.07.07.602435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
F luorogenic ap tamers (FAPs) have become an increasingly important tool in cellular sensing and pathogen diagnostics. However, fine-tuning FAPs for enhanced performance remains challenging even with the structural details provided by X-ray crystallography. Here we present a novel approach to optimize a DNA-based FAP (D-FAP), Lettuce, on repurposed Illumina next-generation sequencing (NGS) chips. When substituting its cognate chromophore, DFHBI-1T, with TO1-biotin, Lettuce not only shows a red-shifted emission peak by 53 nm (from 505 to 558 nm), but also a 4-fold bulk fluorescence enhancement. After screening 8,821 Lettuce variants complexed with TO1-biotin, the C14T mutation is found to exhibit an improved apparent dissociated constant ( vs. 0.82 µM), an increased quantum yield (QY: 0.62 vs. 0.59) and an elongated fluorescence lifetime (τ: 6.00 vs. 5.77 ns), giving 45% more ensemble fluorescence than the canonical Lettuce/TO1-biotin complex. Molecular dynamic simulations further indicate that the π-π stacking interaction is key to determining the coordination structure of TO1-biotin in Lettuce. Our screening-and-simulation pipeline can effectively optimize FAPs without any prior structural knowledge of the canonical FAP/chromophore complexes, providing not only improved molecular probes for fluorescence sensing but also insights into aptamer-chromophore interactions.
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4
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O'Connor E, Micklefield J, Cai Y. Searching for the optimal microbial factory: high-throughput biosensors and analytical techniques for screening small molecules. Curr Opin Biotechnol 2024; 87:103125. [PMID: 38547587 DOI: 10.1016/j.copbio.2024.103125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 06/09/2024]
Abstract
High-throughput screening technologies have been lacking in comparison to the plethora of high-throughput genetic diversification techniques developed in biotechnology. This review explores the challenges and advancements in high-throughput screening for high-value natural products, focusing on the critical need to expand ligand targets for biosensors and increase the throughput of analytical techniques in screening microbial cell libraries for optimal strain performance. The engineering techniques to broaden the scope of ligands for biosensors, such as transcription factors, G protein-coupled receptors and riboswitches are discussed. On the other hand, integration of microfluidics with traditional analytical methods is explored, covering fluorescence-activated cell sorting, Raman-activated cell sorting and mass spectrometry, emphasising recent developments in maximising throughput.
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Affiliation(s)
- Eloise O'Connor
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Jason Micklefield
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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5
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Wang X, Xu N, Zhu L, Yang H, Li C, Tian H, Xu W. Structural Antagonism-Aided Conformational Regulation Enables an Aptamer-Loop G-Quadruplex Modular Sensor of β-Lactoglobulin. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307995. [PMID: 38212277 DOI: 10.1002/smll.202307995] [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: 09/12/2023] [Revised: 12/13/2023] [Indexed: 01/13/2024]
Abstract
A simple, reliable method for identifying β-lactoglobulin (β-LG) in dairy products is needed to protect those with β-LG allergies. A common, practical strategy for target detection is designing simplified nucleic acid nanodevices by integrating functional components. This work presents a label-free modular β-LG aptasensor consisting of an aptamer-loop G-quadruplex (G4), the working conformation of which is regulated by conformational antagonism to ensure respective module functionality and the related signal transduction. The polymorphic conformations of the module-fused sequence are systematically characterized, and the cause is revealed as shifting antagonistic equilibrium. Combined with conformational folding dynamics, this helped regulate functional conformations by fine-tuning the sequences. Furthermore, the principle of specific β-LG detection by parallel G4 topology is examined as binding on the G4 aptamer loop by β-LG to reinforce the G4 topology and fluorescence. Finally, a label-free, assembly-free, succinct, and turn-on fluorescent aptasensor is established, achieving excellent sensitivity across five orders of magnitude, rapidly detecting β-LG within 22-min. This study provides a generalizable approach for the conformational regulation of module-fused G4 sequences and a reference model for creating simplified sensing devices for a variety of targets.
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Affiliation(s)
- Xinxin Wang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
- College of Life Science and Engineering, Handan University, Handan, 056005, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Ning Xu
- School of Life Science, Tsinghua University, Beijing, 100091, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - He Yang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Chen Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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6
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Vallina NS, McRae EKS, Geary C, Andersen ES. An RNA origami robot that traps and releases a fluorescent aptamer. SCIENCE ADVANCES 2024; 10:eadk1250. [PMID: 38507482 PMCID: PMC10954211 DOI: 10.1126/sciadv.adk1250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems.
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Affiliation(s)
| | - Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave, R10-117, Houston, TX 77030, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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7
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [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: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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8
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Hoeher JE, Sande NE, Widom JR. Probing and perturbing riboswitch folding using a fluorescent base analogue. Photochem Photobiol 2024; 100:419-433. [PMID: 38098287 PMCID: PMC10950518 DOI: 10.1111/php.13896] [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: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 03/20/2024]
Abstract
Riboswitches are mRNA segments that regulate gene expression in response to ligand binding. The Class I preQ1 riboswitch consists of a stem-loop and an adenine-rich single-stranded tail ("L3"), which adopt a pseudoknot structure upon binding of the ligand preQ1 . We inserted 2-aminopurine (2-AP), a fluorescent analogue of adenine (A), into the riboswitch at six different positions within L3. Here, 2-AP functions both as a spectroscopic probe and as a "mutation" that reveals how alteration of specific A residues impacts the riboswitch. Using fluorescence and circular dichroism spectroscopy, we found that 2-AP decreases the affinity of the riboswitch for preQ1 at all labeling positions tested, although modified and unmodified variants undergo the same global conformational changes at sufficiently high preQ1 concentration. 2-AP substitution is most detrimental to ligand binding at sites proximal to the ligand-binding pocket, while distal labeling sites exhibit the largest impacts on the stability of the L3 domain in the absence of ligand. Insertion of multiple 2-AP residues does not induce significant additional disruptions. Our results show that interactions involving the A residues in L3 play a critical role in ligand recognition by the preQ1 riboswitch and that 2-AP substitution exerts complex and varied impacts on this riboswitch.
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Affiliation(s)
- Janson E. Hoeher
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
| | - Natalie E. Sande
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
| | - Julia R. Widom
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
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9
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Legen T, Mayer G. Modular Approach for Rapid Identification of RNA-Based Sensors. ACS Sens 2024; 9:753-758. [PMID: 38253513 DOI: 10.1021/acssensors.3c02060] [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: 01/24/2024]
Abstract
Detection of metabolites in real time and in whole cells requires effective molecular sensors. In this regard, fluorogenic light-up RNAs have recently become important tools for small-molecule detection in cells. However, the construction of light-up RNA sensors is an arduous task that requires structural knowledge of both the sensor and reporter RNA. De novo strategies for selecting sensors from RNA libraries are limited and are mostly restricted to known aptamers and riboswitches. Here, we provide a solution to this problem by developing a capture-SELEX variant that allows the obtained libraries and aptamers to be linked to fluorogenic RNAs in a modular and allosteric manner. The approach is generally applicable and allows for rapid modular allosteric assembly with green- or red-shifted fluorogenic RNAs.
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Affiliation(s)
- Tjasa Legen
- Life and Medical Sciences, University of Bonn, 53121 Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences, University of Bonn, 53121 Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, 53121 Bonn, Germany
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10
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Ji R, Wang L, Shang Y, Du S, Xiao Y, Dong W, Cui L, Gao R, Ren K. RNA Condensate as a Versatile Platform for Improving Fluorogenic RNA Aptamer Properties and Cell Imaging. J Am Chem Soc 2024; 146:4402-4411. [PMID: 38329936 DOI: 10.1021/jacs.3c09162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Fluorogenic RNA aptamers are valuable tools for cell imaging, but they still suffer from shortcomings such as easy degradation, limited photostability, and low fluorescence enhancement. Molecular crowding conditions enable the stabilization of the structure, promotion of folding, and improvement of activity of functional RNA. Based on artificial RNA condensates, here we present a versatile platform to improve fluorogenic RNA aptamer properties and develop sensors for target analyte imaging in living cells. Using the CUG repeat as a general tag to drive phase separation, various fluorogenic aptamer-based RNA condensates (FLARE) were prepared. We show that the molecular crowding of FLARE can improve the enzymatic resistance, thermostability, photostability, and binding affinity of fluorogenic RNA aptamers. Moreover, the FLARE systems can be modularly engineered into sensors (FLARES), which demonstrate enhanced brightness and sensitivity compared to free sensors dispersed in homogeneous solution. This scalable design principle provides new insights into RNA aptamer property regulation and cellular imaging.
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Affiliation(s)
- Ruoyang Ji
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Long Wang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Yuzhe Shang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Songyuan Du
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Yang Xiao
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Wei Dong
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P.R. China
| | - Ruru Gao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, P.R. China
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11
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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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12
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Yin P, Ge M, Xie S, Zhang L, Kuang S, Nie Z. A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers. Chem Sci 2023; 14:14131-14139. [PMID: 38098702 PMCID: PMC10717586 DOI: 10.1039/d3sc04957d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of gene expression at the post-transcriptional level, offering valuable insights into disease mechanisms and prospects for targeted therapeutic interventions. Herein, we present a class of miRNA-induced light-up RNA sensors (miLS) that are founded on the toehold mediated principle and employ the fluorogenic RNA aptamers Pepper and Squash as imaging modules. By incorporating a sensor switch to disrupt the stabilizing stem of these aptamers, our design offers enhanced flexibility and convertibility for different target miRNAs and aptamers. These sensors detect multiple miRNA targets (miR-21 and miR-122) with detection limits of 0.48 and 0.2 nM, respectively, while achieving a robust signal-to-noise ratio of up to 44 times. Capitalizing on the distinct fluorescence imaging channels afforded by Pepper-HBC620 (red) and Squash-DFHBI-1T (green), we establish an orthogonal miRNA activation imaging platform, enabling the simultaneous visualization of different intracellular miRNAs in living cells. Our dual-color orthogonal miLS imaging platform provides a powerful tool for sequence-specific miRNA imaging in different cells, opening up new avenues for studying the intricate functions of RNA in living cells.
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Affiliation(s)
- Peng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Mingmin Ge
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Li Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University Changsha 410082 China
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13
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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14
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Wang T, Simmel FC. Switchable Fluorescent Light-Up Aptamers Based on Riboswitch Architectures. Angew Chem Int Ed Engl 2023; 62:e202302858. [PMID: 37163453 DOI: 10.1002/anie.202302858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Fluorescent light-up RNA aptamers (FLAPs) such as Spinach or Mango can bind small fluorogens and activate their fluorescence. Here, we adopt a switching mechanism otherwise found in riboswitches and use it to engineer switchable FLAPs that can be activated or repressed by trigger oligonucleotides or small metabolites. The fluorophore binding pocket of the FLAPs comprises guanine (G) quadruplexes, whose critical nucleotides can be sequestered by corresponding anti-FLAP sequences, leading to an inactive conformation and thus preventing association with the fluorophore. We modified the FLAPs with designed toehold hairpins that carry either an anti-FLAP or an anti-anti-FLAP sequence within the loop region. The addition of an input RNA molecule triggers a toehold-mediated strand invasion process that refolds the FLAP into an active or inactive configuration. Several of our designs display close-to-zero leak signals and correspondingly high ON/OFF fluorescence ratios. We also modified purine aptamers to sequester a partial anti-FLAP or an anti-anti-FLAP sequence to control the formation of the fluorogen-binding conformation, resulting in FLAPs whose fluorescence is activated or deactivated in the presence of guanine or adenine. We demonstrate that switching modules can be easily combined to generate FLAPs whose fluorescence depends on several inputs with different types of input logic.
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Affiliation(s)
- Tianhe Wang
- Physics of Synthetic Biological Systems-E14, Department of Bioscience, TUM School of Natural Science, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems-E14, Department of Bioscience, TUM School of Natural Science, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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15
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Chen Z, Chen W, Reheman Z, Jiang H, Wu J, Li X. Genetically encoded RNA-based sensors with Pepper fluorogenic aptamer. Nucleic Acids Res 2023; 51:8322-8336. [PMID: 37486780 PMCID: PMC10484673 DOI: 10.1093/nar/gkad620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023] Open
Abstract
Sensors to measure the abundance and signaling of intracellular molecules are crucial for understanding their physiological functions. Although conventional fluorescent protein-based sensors have been designed, RNA-based sensors are promising imaging tools. Numerous RNA-based sensors have been developed. These sensors typically contain RNA G-quadruplex (RG4) motifs and thus may be suboptimal in living cells. Here we describe RNA-based sensors based on Pepper, a fluorogenic RNA without an RG4 motif. With Pepper, we engineered various sensors for metabolites, synthetic compounds, proteins and metal ions in vitro and in living cells. In addition, these sensors show high activation and selectivity, demonstrating their universality and robustness. In the case of sensors responding to S-adenosylmethionine (SAM), a metabolite produced by methionine adenosyltransferase (MATase), we showed that our sensors exhibited positively correlated fluorescence responding to different SAM levels. Importantly, we revealed the SAM biosynthesis pathway and monitored MATase activity and gene expression spatiotemporally in living individual human cells. Additionally, we constructed a ratiometric SAM sensor to determine the inhibition efficacy of a MATase inhibitor in living cells. Together, these sensors comprising Pepper provide a useful platform for imaging diverse cellular targets and their signaling pathway.
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Affiliation(s)
- Zhenyin Chen
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China
- Department of Pulmonary and Critical Care Medicine, Department of Inflammation and Clinical Allergology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Chen
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Cytology and Genetics, the Hengyang Key Laboratory of Cellular Stress Biology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhayila Reheman
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, Hebei University, Baoding, Hebei 071000, China
| | - Haodong Jiang
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahui Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA01003, USA
| | - Xing Li
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China
- Department of Pulmonary and Critical Care Medicine, Department of Inflammation and Clinical Allergology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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16
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Wakchaure PD, Ganguly B. Exploring the structure, function of thiamine pyrophosphate riboswitch, and designing small molecules for antibacterial activity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1774. [PMID: 36594112 DOI: 10.1002/wrna.1774] [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: 09/15/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023]
Abstract
During the last decade, riboswitches emerged as new small-molecule sensing RNA in bacteria. Thiamine pyrophosphate (TPP) riboswitch is widely distributed and occurs in plants, bacteria, fungi, and archaea. Extensive biochemical, structural, and genetic studies have been carried out to elucidate the recognition mechanism of TPP riboswitches. However, a comprehensive report summarizing all information on recognition principles and newly designed ligands for TPP riboswitch is scarce in the literature. This review gives a comprehensive understanding of the TPP riboswitch's structure, mechanism, and methods applied to design ligands for the TPP riboswitch. The ligand-bound TPP riboswitch was studied with various experimental and theoretical techniques to elucidate the conformational dynamics. The mutation studies shed light on the significance of pyrimidine sensing helix for the binding of ligands. Further, the structure-activity relationship study and fragment-based approach lead to the development of ligands with Kd values at the sub-micromolar level. However, there is a need to design more potent inhibitors for TPP riboswitch for therapeutic applications. The recent advancements in ligand design highlight the TPP riboswitch as a promising target for developing new antibiotics. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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17
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Chingarande RG, Tian K, Kuang Y, Sarangee A, Hou C, Ma E, Ren J, Hawkins S, Kim J, Adelstein R, Chen S, Gillis KD, Gu LQ. Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor. Proc Natl Acad Sci U S A 2023; 120:e2108118120. [PMID: 37276386 PMCID: PMC10268594 DOI: 10.1073/pnas.2108118120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.
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Affiliation(s)
- Rugare G. Chingarande
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Kai Tian
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Yu Kuang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Aby Sarangee
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Chengrui Hou
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Emily Ma
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Jarett Ren
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sam Hawkins
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Joshua Kim
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Ray Adelstein
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sally Chen
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Kevin D. Gillis
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Li-Qun Gu
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
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18
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Fang M, Li H, Xie X, Wang H, Jiang Y, Li T, Zhang B, Jiang X, Cao Y, Zhang R, Zhang D, Zhao Y, Zhu L, Chen X, Yang Y. Imaging intracellular metabolite and protein changes in live mammalian cells with bright fluorescent RNA-based genetically encoded sensors. Biosens Bioelectron 2023; 235:115411. [PMID: 37236014 DOI: 10.1016/j.bios.2023.115411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/07/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
Fluorescent RNA (FR)-based genetically encoded sensors have been engineered to detect various essential metabolites in living systems. However, the unfavorable characteristics of FR impede sensor applications. Here, we describe a strategy for converting Pepper fluorescent RNA into a series of fluorescent sensors to detect their cognate targets both in vitro and in live cells. Compared to previously developed FR-based sensors, Pepper-based sensors exhibited expanded emission of up to 620 nm and markedly improved cellular brightness, allowing robust and real-time monitoring of the pharmacologic-triggered dynamics changes in the intracellular level of S-adenosylmethionine (SAM) and the optogenetic manipulated protein translocation in live mammalian cells. Furthermore, signal amplification in fluorescence imaging of the target was achieved using the CRISPR-display strategy by incorporating a Pepper-based sensor into the sgRNA scaffold. Together, these results demonstrate that Pepper can be readily developed into high-performance FR-based sensors to detect various cellular targets.
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Affiliation(s)
- Mengyue Fang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Huiwen Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xin Xie
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Hui Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Ying Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Tianyu Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Bibi Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xin Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yueyang Cao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Rui Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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19
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Qi Q, Liu X, Fu F, Shen W, Cui S, Yan S, Zhang Y, Du Y, Tian T, Zhou X. Utilizing Epigenetic Modification as a Reactive Handle To Regulate RNA Function and CRISPR-Based Gene Regulation. J Am Chem Soc 2023; 145:11678-11689. [PMID: 37191624 DOI: 10.1021/jacs.3c01864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The current methods to control RNA functions in living conditions are limited. The new RNA-controlling strategy presented in this study involves utilizing 5-formylcytidine (f5C)-directed base manipulation. This study shows that malononitrile and pyridine boranes can effectively manipulate the folding, small molecule binding, and enzyme recognition of f5C-bearing RNAs. We further demonstrate the efficiency of f5C-directed reactions in controlling two different clustered regularly interspaced short palindromic repeat (CRISPR) systems. Although further studies are needed to optimize the efficiency of these reactions in vivo, this small molecule-based approach presents exciting new opportunities for regulating CRISPR-based gene expression and other applications.
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Affiliation(s)
- Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Fang Fu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Wei Shen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Shuangyu Cui
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Shen Yan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Yutong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Yuhao Du
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China
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20
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Ortega AD. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors. Biomolecules 2023; 13:biom13050765. [PMID: 37238635 DOI: 10.3390/biom13050765] [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: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
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Affiliation(s)
- Alvaro Darío Ortega
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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21
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Yoshikawa AM, Rangel AE, Zheng L, Wan L, Hein LA, Hariri AA, Eisenstein M, Soh HT. A massively parallel screening platform for converting aptamers into molecular switches. Nat Commun 2023; 14:2336. [PMID: 37095144 PMCID: PMC10126150 DOI: 10.1038/s41467-023-38105-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/14/2023] [Indexed: 04/26/2023] Open
Abstract
Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.
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Affiliation(s)
- Alex M Yoshikawa
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Liwei Zheng
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Leighton Wan
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Linus A Hein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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22
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Husser C, Vuilleumier S, Ryckelynck M. FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205232. [PMID: 36436882 DOI: 10.1002/smll.202205232] [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: 08/25/2022] [Revised: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.
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Affiliation(s)
- Claire Husser
- CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, UPR 9002, 2 allée Konrad Roentgen, Strasbourg, 67000, France
| | - Stéphane Vuilleumier
- CNRS, Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR 7156, 4 allée Konrad Roentgen, Strasbourg, 67000, France
| | - Michael Ryckelynck
- CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, UPR 9002, 2 allée Konrad Roentgen, Strasbourg, 67000, France
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23
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Mi L, Yu Q, Mudiyanselage APK, Wu R, Sun Z, Zheng R, Ren K, You M. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. ACS Sens 2023; 8:308-316. [PMID: 36608281 PMCID: PMC10630924 DOI: 10.1021/acssensors.2c02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.
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Affiliation(s)
- Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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24
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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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25
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Dong X, Qi S, Khan IM, Sun Y, Zhang Y, Wang Z. Advances in riboswitch-based biosensor as food samples detection tool. Compr Rev Food Sci Food Saf 2023; 22:451-472. [PMID: 36511082 DOI: 10.1111/1541-4337.13077] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/09/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022]
Abstract
Food safety has always been a hot issue of social concern, and biosensing has been widely used in the field of food safety detection. Compared with traditional aptamer-based biosensors, aptamer-based riboswitch biosensing represents higher precision and programmability. A riboswitch is an elegant example of controlling gene expression, where the target is coupled to the aptamer domain, resulting in a conformational change in the downstream expression domain and determining the signal output. Riboswitch-based biosensing can be extensively applied to the portable real-time detection of food samples. The numerous key features of riboswitch-based biosensing emphasize their sustainability, renewable, and testing, which promises to transform engineering applications in the field of food safety. This review covers recent developments in riboswitch-based biosensors. The brief history, definition, and modular design (regulatory mode, reporter, and expression platform) of riboswitch-based biosensors are explained for better insight into the design and construction. We summarize recent advances in various riboswitch-based biosensors involving theophylline, malachite green, tetracycline, neomycin, fluoride, thrombin, naringenin, ciprofloxacin, and paromomycin, aiming to provide general guidance for the design of riboswitch-based biosensors. Finally, the challenges and prospects are also summarized as a way forward stratagem and signs of progress.
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Affiliation(s)
- Xiaoze Dong
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Shuo Qi
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yuhan Sun
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Collaborative innovation center of food safety and quality control in Jiangsu Province, Food, Jiangnan University, Wuxi, China
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26
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High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics. Methods Mol Biol 2023; 2570:243-269. [PMID: 36156788 DOI: 10.1007/978-1-0716-2695-5_19] [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: 01/25/2023]
Abstract
Small-molecule sensing is a major issue as they can serve both in fundamental science and as makers of various diseases, contaminations, or even environment pollution. RNA aptamers are single-stranded nucleic acids that can adopt different conformations and specifically recognize a wide range of ligands, making them good candidates to develop biosensors of small molecules. Recently, light-up RNA aptamers have been introduced and used as starting building blocks of RNA-based fluorogenic biosensors. They are typically made of three domains: a reporter domain (a light-up aptamer), connected to a sensor domain (another aptamer) via a communication module. The latter is instrumental as being in charge of information transmission between the sensor and the reporting domains. Here we present an ultrahigh-throughput screening procedure to develop RNA-based fluorogenic biosensors by selecting optimized communication modules through an exhaustive functional exploration of every possible sequence permutation using droplet-based microfluidics and next-generation sequencing.
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27
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Wu Y, Zhu L, Li S, Chu H, Wang X, Xu W. High content design of riboswitch biosensors: All-around rational module-by-module design. Biosens Bioelectron 2022; 220:114887. [DOI: 10.1016/j.bios.2022.114887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/27/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
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28
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Xu J, Cotruvo JA. Reconsidering the czcD (NiCo) Riboswitch as an Iron Riboswitch. ACS BIO & MED CHEM AU 2022; 2:376-385. [PMID: 35996475 PMCID: PMC9389577 DOI: 10.1021/acsbiomedchemau.1c00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Recent work has proposed
a new mechanism of bacterial iron regulation:
riboswitches that undergo a conformational change in response to FeII. The czcD (NiCo) riboswitch was initially
proposed to be specific for NiII and CoII, but
we recently showed via a czcD-based fluorescent sensor
that FeII is also a plausible physiological ligand for
this riboswitch class. Here, we provide direct evidence that this
riboswitch class responds to FeII. Isothermal titration
calorimetry studies of the native czcD riboswitches
from three organisms show no response to MnII, a weak response
to ZnII, and similar dissociation constants (∼1
μM) and conformational responses for FeII, CoII, and NiII. Only the iron response is in the physiological
concentration regime; the riboswitches’ responses to CoII, NiII, and ZnII require 103-, 105-, and 106-fold higher “free”
metal ion concentrations, respectively, than the typical availability
of those metal ions in cells. By contrast, the “Sensei”
RNA, recently claimed to be an iron-specific riboswitch, exhibits
no response to FeII. Our results demonstrate that iron
responsiveness is a conserved property of czcD riboswitches
and clarify that this is the only family of iron-responsive riboswitch
identified to date, setting the stage for characterization of their
physiological function.
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Affiliation(s)
- Jiansong Xu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph A. Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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29
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Mumbleau MM, Meyer MR, Hammond MC. Determination of In Vitro and Cellular Turn-on Kinetics for Fluorogenic RNA Aptamers. J Vis Exp 2022:10.3791/64367. [PMID: 36036622 PMCID: PMC9701086 DOI: 10.3791/64367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Abstract
Fluorogenic RNA aptamers have been applied in live cells to tag and visualize RNAs, report on gene expression, and activate fluorescent biosensors that detect levels of metabolites and signaling molecules. In order to study dynamic changes in each of these systems, it is desirable to obtain real-time measurements, but the accuracy of the measurements depends on the kinetics of the fluorogenic reaction being faster than the sampling frequency. Here, we describe methods to determine the in vitro and cellular turn-on kinetics for fluorogenic RNA aptamers using a plate reader equipped with a sample injector and a flow cytometer, respectively. We show that the in vitro kinetics for the fluorescence activation of the Spinach2 and Broccoli aptamers can be modeled as two-phase association reactions and have differing fast phase rate constants of 0.56 s-1 and 0.35 s-1, respectively. In addition, we show that the cellular kinetics for the fluorescence activation of Spinach2 in Escherichia coli, which is further limited by dye diffusion into the Gram-negative bacteria, is still sufficiently rapid to enable accurate sampling frequency on the minute timescale. These methods to analyze fluorescence activation kinetics are applicable to other fluorogenic RNA aptamers that have been developed.
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Affiliation(s)
- Madeline M Mumbleau
- Department of Chemistry and Henry Eyring Center for Cell & Genome Science, University of Utah
| | - Madeline R Meyer
- Department of Chemistry and Henry Eyring Center for Cell & Genome Science, University of Utah
| | - Ming C Hammond
- Department of Chemistry and Henry Eyring Center for Cell & Genome Science, University of Utah;
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30
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Liu XH, Li BR, Ying ZM, Tang LJ, Wang F, Jiang JH. Small-Molecule-Mediated Split-Aptamer Assembly for Inducible CRISPR-dCas9 Transcription Activation. ACS Chem Biol 2022; 17:1769-1777. [PMID: 35700146 DOI: 10.1021/acschembio.2c00101] [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: 11/28/2022]
Abstract
Inducible CRISPR-dCas9 transcription system has become a powerful tool for transcription regulation and sensing. Here, we develop a new concept of small-molecule-mediated split-aptamer assembly for inducible CRISPR-dCas9 transcription activation, allowing quantitative detection and imaging of S-adenosyl methionine (SAM) in live cells. This inducible transcription system is designed by integrating one fragment of a split SAM aptamer to guide RNA (gRNA) and the other to MS2 arrays. SAM-mediated reassembly of the split fragments recruits an MCP-fused transcription activator to the gRNA-dCas9 complex, activating the expression of a near-infrared fluorescent protein for imaging. We demonstrate that this inducible transcription system achieves quantitative detection of SAM with high sensitivity in live cells. Our system shows that methionine adenosyltransferase 1A (MAT1A) and MAT2A can both catalyze SAM production in live cells and the SAM levels in cancer cells can be increased via upregulation of MAT1A mRNA by epigenetic inhibitors. This split-aptamer assembly strategy could afford a new approach for controlling the CRISPR-dCas9 system, enabling conditional transcription regulation in response to endogenous metabolites in live cells.
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Affiliation(s)
- Xiao-Han Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Bang-Rui Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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31
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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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32
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Peng Y, Ai X, Peng B. Trans-cleaving hammerhead ribozyme in specific regions can improve knockdown efficiency in vivo. J Cell Biochem 2022. [PMID: 35411616 DOI: 10.1002/jcb.30249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/06/2022] [Accepted: 03/28/2022] [Indexed: 11/08/2022]
Abstract
Trans-cleaving techniques have been most enthusiastically embraced in the development of therapy for genetic diseases, particularly in the correction of monogenic recessive mutations at the messenger RNA level. However, easy degradation and poor catalytic activity in vivo remain significant obstacles to trans-cleaving of the hammerhead ribozyme. Herein, we found a novel scaffold RNA that stabilizes the ribozyme structure in trans-cleaving and promotes the knockdown efficiency of the hammerhead ribozyme in specific regions of living cells. We can give the trans-cleaving hammerhead ribozyme the ability to knock down specific genes in specific cell regions by changing different scaffolds. Therefore, our study proves the potential usefulness of the RNA knockdown strategy with high-specific trans-cleaving hammerhead ribozyme as a therapeutic approach in gene therapy.
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Affiliation(s)
- Yan Peng
- Medical School, Fuyang Normal University, Fuyang, Anhui, China
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xilei Ai
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Peng
- College of Life Science and Resources and Environment, Yichun University, Yichun, Jiangxi, China
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33
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A system for multiplexed selection of aptamers with exquisite specificity without counterselection. Proc Natl Acad Sci U S A 2022; 119:e2119945119. [PMID: 35290115 PMCID: PMC8944265 DOI: 10.1073/pnas.2119945119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aptamers have the capacity to discriminate between structurally similar small molecules. However, generating such highly specific aptamers has proven challenging using conventional processes based on counterselection against nontarget molecules. In this work, we describe a high-throughput screening platform that can characterize the specificity of millions of aptamers toward a group of structurally related molecules in a single experiment and generate exquisitely specific aptamers without any counterselection. As exemplars, we generated aptamers with high affinity and specificity toward three structurally related kynurenine metabolites using our platform. Our platform can be readily adapted to other small-molecule targets and should therefore accelerate the development of aptamer reagents with exquisite specificity. Aptamers have proven to be valuable tools for the detection of small molecules due to their remarkable ability to specifically discriminate between structurally similar molecules. Most aptamer selection efforts have relied on counterselection to eliminate aptamers that exhibit unwanted cross-reactivity to interferents or structurally similar relatives to the target of interest. However, because the affinity and specificity characteristics of an aptamer library are fundamentally unknowable a priori, it is not possible to determine the optimal counterselection parameters. As a result, counterselection experiments require trial-and-error approaches that are inherently inefficient and may not result in aptamers with the best combination of affinity and specificity. In this work, we describe a high-throughput screening process for generating high-specificity aptamers to multiple targets in parallel while also eliminating the need for counterselection. We employ a platform based on a modified benchtop sequencer to conduct a massively parallel aptamer screening process that enables the selection of highly specific aptamers against multiple structurally similar molecules in a single experiment, without any counterselection. As a demonstration, we have selected aptamers with high affinity and exquisite specificity for three structurally similar kynurenine metabolites that differ by a single hydroxyl group in a single selection experiment. This process can easily be adapted to other small-molecule analytes and should greatly accelerate the development of aptamer reagents that achieve exquisite specificity for their target analytes.
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34
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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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35
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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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36
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Zheng G, Zhao L, Yuan D, Li J, Yang G, Song D, Miao H, Shu L, Mo X, Xu X, Li L, Song X, Zhao Y. A genetically encoded fluorescent biosensor for monitoring ATP in living cells with heterobifunctional aptamers. Biosens Bioelectron 2022; 198:113827. [PMID: 34861524 DOI: 10.1016/j.bios.2021.113827] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 02/08/2023]
Abstract
Visualizing the dynamics of ATP in living cells is key to understanding cellular energy metabolism and related diseases. However, the live-cell applications of current methods are still limited due to challenges in biological compatibility and sensitivity to pH. Herein, a novel label-free fluorescent " turn-on " biosensor for monitoring ATP in living bacterias and mammalian cells was developed. This biosensor (Broc-ATP) employed heterobifunctional aptamers to detect ATP with high sensitivity in vitro. In our system, a very useful tandem method was established by combining four Broc-ATPs with 3 × F30 three-way junction scaffold to construct an intracellular biosensor that achieves sufficient fluorescence to respond to intracellular ATP. This intracellular biosensor can be used for sensitive and specific dynamic imaging of ATP in mammalian cells. Hence, this genetically encoded biosensor provides a robust and efficient tool for the detection of intracellular ATP dynamics and 3 × F30 tandem method expands the application of heterobifunctional aptamers in mammalian cells.
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Affiliation(s)
- Guoliang Zheng
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Liang Zhao
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Deyu Yuan
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Jia Li
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Gang Yang
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Danxia Song
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Hui Miao
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Linjuan Shu
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Ling Li
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China.
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China.
| | - Yongyun Zhao
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China.
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37
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Kaczmarek JA, Prather KLJ. Effective use of biosensors for high-throughput library screening for metabolite production. J Ind Microbiol Biotechnol 2021; 48:6339276. [PMID: 34347108 PMCID: PMC8788864 DOI: 10.1093/jimb/kuab049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022]
Abstract
The development of fast and affordable microbial production from recombinant pathways is a challenging endeavor, with targeted improvements difficult to predict due to the complex nature of living systems. To address the limitations in biosynthetic pathways, much work has been done to generate large libraries of various genetic parts (promoters, RBSs, enzymes, etc.) to discover library members that bring about significantly improved levels of metabolite production. To evaluate these large libraries, high throughput approaches are necessary, such as those that rely on biosensors. There are various modes of operation to apply biosensors to library screens that are available at different scales of throughput. The effectiveness of each biosensor-based method is dependent on the pathway or strain to which it is applied, and all approaches have strengths and weaknesses to be carefully considered for any high throughput library screen. In this review, we discuss the various approaches used in biosensor screening for improved metabolite production, focusing on transcription factor-based biosensors.
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Affiliation(s)
- Jennifer A Kaczmarek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02142, USA
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38
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Riboswitch RS thiT as a molecular tool in Lactococcus lactis. Appl Environ Microbiol 2021; 88:e0176421. [PMID: 34936833 PMCID: PMC8862789 DOI: 10.1128/aem.01764-21] [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] [Indexed: 12/02/2022] Open
Abstract
Previous RNA sequencing has allowed the identification of 129 long 5′ untranslated regions (UTRs) in the Lactococcus lactis MG1363 transcriptome. These sequences potentially harbor cis-acting riboswitches. One of the identified extended 5′ UTRs is a putative thiamine pyrophosphate (TPP) riboswitch. It is located immediately upstream of the thiamine transporter gene thiT (llmg_0334). To confirm this assumption, the 5′-UTR sequence was placed upstream of the gene encoding the superfolder green fluorescent protein (sfGFP), sfgfp, allowing the examination of the expression of sfGFP in the presence or absence of thiamine in the medium. The results show that this sequence indeed represents a thiamine-responsive TPP riboswitch. This RNA-based genetic control device was used to successfully restore the mutant phenotype of an L. lactis strain lacking the major autolysin gene, acmA. The L. lactisthiT TPP riboswitch (RSthiT) is a useful molecular genetic tool enabling the gradual downregulation of the expression of genes under its control by adjusting the thiamine concentration. IMPORTANCE The capacity of microbes with biotechnological importance to adapt to and survive under quickly changing industrial conditions depends on their ability to adequately control gene expression. Riboswitches are important RNA-based elements involved in rapid and precise gene regulation. Here, we present the identification of a natural thiamine-responsive riboswitch of Lactococcus lactis, a bacterium used worldwide in the production of dairy products. We used it to restore a genetic defect in an L. lactis mutant and show that it is a valuable addition to the ever-expanding L. lactis genetic toolbox.
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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40
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Moon JD, Wu J, Dey SK, Litke JL, Li X, Kim H, Jaffrey SR. Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors. Cell Chem Biol 2021; 28:1569-1580.e4. [PMID: 34010626 PMCID: PMC8573057 DOI: 10.1016/j.chembiol.2021.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Small molecules can be imaged in living cells using biosensors composed of RNA. However, RNA-based devices are difficult to design. Here, we describe a versatile platform for designing RNA-based fluorescent small-molecule sensors using naturally occurring highly stable three-way junction RNAs. We show that ligand-binding aptamers and fluorogenic aptamers can be inserted into three-way junctions and connected in a way that enables the three-way junction to function as a small-molecule-regulated fluorescent sensor in vitro and in cells. The sensors are designed so that the interhelical stabilizing interactions in the three-way junction are only induced upon ligand binding. We use these RNA-based devices to measure the dynamics of S-adenosylmethionine levels in mammalian cells in real time. We show that this strategy is compatible with diverse metabolite-binding RNA aptamers, fluorogenic aptamers, and three-way junctions. Overall, these data demonstrate a versatile method for readily generating RNA devices that function in living cells.
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Affiliation(s)
- Jared D Moon
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Jiahui Wu
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Sourav K Dey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Jacob L Litke
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Xing Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Hyaeyeong Kim
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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41
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Rational Design of Allosteric Fluorogenic RNA Sensors for Cellular Imaging. Methods Mol Biol 2021. [PMID: 34086279 DOI: 10.1007/978-1-0716-1499-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescence-based tools are invaluable in studying cellular functions. Traditional small molecule or protein-based fluorescent sensors have been widely used for the cellular imaging, but the choice of targets is still limited. Recently, fluorogenic RNA-based sensors gained lots of attention. This novel sensor system can function as a general platform for various cellular targets. Here, we describe the steps to rationally design, optimize, and apply fluorogenic RNA-based sensors, using the intracellular imaging of tetracycline in living E. coli cells as an example.
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42
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Gu Y, Huang LJ, Zhao W, Zhang TT, Cui MR, Yang XJ, Zhao XL, Chen HY, Xu JJ. Living-Cell MicroRNA Imaging with Self-Assembling Fragments of Fluorescent Protein-Mimic RNA Aptamer. ACS Sens 2021; 6:2339-2347. [PMID: 34028262 DOI: 10.1021/acssensors.1c00453] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As the cellular roles of RNA abundance continue to increase, there is an urgent need for the corresponding tools to elucidate native RNA functions and dynamics, especially those of short, low-abundance RNAs in live cells. Fluorescent RNA aptamers provide a useful strategy to create the RNA tag and biosensor devices. Corn, which binds with 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO), is a good candidate for the RNA tag because of its enhanced photostability and red-shifted spectrum. Herein, we report for the first time the utilization of Corn as a split aptamer system, combined with RNA-initiated fluorescence complementation (RIFC), for monitoring RNA self-assembly and sensing microRNA. In this platform, the 28-nt Corn was divided into two nonfunctional halves (named probe I and probe II), and an additional target RNA recognition and stem part was introduced in each probe. The target RNA can trigger the self-assembly reconstitution of the Corn's G-quadruplex scaffold for DFHO binding and turn-on fluorescence. These probes can be transfected stably into mammalian cells and deliver the light-up fluorescent response to microRNA-21 (miR-21). Significantly, the probes have good photostability, with minimal fluorescence loss after continuous irradiation, and can be used for imaging of miR-21 in living mammalian cells. The proposed method is universal and could be applied to the sensing of other tumor-associated RNAs, including messenger RNA and noncoding RNA, as well as for monitoring RNA/RNA interactions. The Corn-based splitting aptamers show promising potential in the real-time visualization and mechanistic analysis of nucleic acids.
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Affiliation(s)
- Yu Gu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Institute for Materials Science and Engineering, School of Materials Sciences and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Li-Juan Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ting-Ting Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mei-Rong Cui
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue-Jiao Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue-Li Zhao
- College of Chemistry and Molecular Engineering, Zheng-Zhou University, Zhengzhou 450001, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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43
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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44
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Ortega AD, Takhaveev V, Vedelaar SR, Long Y, Mestre-Farràs N, Incarnato D, Ersoy F, Olsen LF, Mayer G, Heinemann M. A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux. Cell Chem Biol 2021; 28:1554-1568.e8. [PMID: 33915105 DOI: 10.1016/j.chembiol.2021.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/25/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022]
Abstract
RNA-based sensors for intracellular metabolites are a promising solution to the emerging issue of metabolic heterogeneity. However, their development, i.e., the conversion of an aptamer into an in vivo-functional intracellular metabolite sensor, still harbors challenges. Here, we accomplished this for the glycolytic flux-signaling metabolite, fructose-1,6-bisphosphate (FBP). Starting from in vitro selection of an aptamer, we constructed device libraries with a hammerhead ribozyme as actuator. Using high-throughput screening in yeast with fluorescence-activated cell sorting (FACS), next-generation sequencing, and genetic-environmental perturbations to modulate the intracellular FBP levels, we identified a sensor that generates ratiometric fluorescent readout. An abrogated response in sensor mutants and occurrence of two sensor conformations-revealed by RNA structural probing-indicated in vivo riboswitching activity. Microscopy showed that the sensor can differentiate cells with different glycolytic fluxes within yeast populations, opening research avenues into metabolic heterogeneity. We demonstrate the possibility to generate RNA-based sensors for intracellular metabolites for which no natural metabolite-binding RNA element exits.
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Affiliation(s)
- Alvaro Darío Ortega
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Silke Roelie Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Yi Long
- LIMES Institute, University of Bonn, 53121 Bonn, Germany; Institute of Biochemistry and Molecular Biology, University of Southern Denmark, DK5230 Odense M, Denmark
| | - Neus Mestre-Farràs
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Danny Incarnato
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | | | - Lars Folke Olsen
- Institute of Biochemistry and Molecular Biology, University of Southern Denmark, DK5230 Odense M, Denmark
| | - Günter Mayer
- LIMES Institute, University of Bonn, 53121 Bonn, Germany; Center of Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands.
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Abstract
Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.
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Affiliation(s)
- Huangmei Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, China.,NYU-ECNU Institute of Physics at NYU Shanghai, Shanghai, China
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46
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Abstract
The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity of their photophysical characterisation, this paper is a model study on Baby Spinach, a truncated Spinach aptamer with half its sequence. Fluorescence and fluorescence excitation spectra of DFHBI complexes of Spinach and Baby Spinach are known to be similar. Surprisingly, a significant divergence between absorption and fluorescence excitation spectra of the DFHBI/RNA complex was observed on conditions of saturation at large excess of RNA over DFHBI. Since absorption spectra were not reported for any Spinach-type aptamer, this effect is new. Quantitative modelling of the absorption spectrum based on competing dark and fluorescent binding sites could explain it. However, following reasoning of fluorescence lifetimes of bound DFHBI, femtosecond-fluorescence lifetime profiles would be more supportive of the notion that the abnormal absorption spectrum is largely caused by trans-isomers formed within the cis-bound DFHBI/RNA complex. Independent of the origin, the unexpected discrepancy between absorption and fluorescence excitation spectra allows for easily accessed screening and insight into the efficiency of a fluorogenic dye/RNA system.
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47
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Manna S, Truong J, Hammond MC. Guanidine Biosensors Enable Comparison of Cellular Turn-on Kinetics of Riboswitch-Based Biosensor and Reporter. ACS Synth Biol 2021; 10:566-578. [PMID: 33646758 PMCID: PMC7985839 DOI: 10.1021/acssynbio.0c00583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 12/30/2022]
Abstract
Cell-based sensors are useful for many synthetic biology applications, including regulatory circuits, metabolic engineering, and diagnostics. While considerable research efforts have been made toward recognizing new target ligands and increasing sensitivity, the analysis and optimization of turn-on kinetics is often neglected. For example, to our knowledge there has been no systematic study that compared the performance of a riboswitch-based biosensor versus reporter for the same ligand. In this study, we show the development of RNA-based fluorescent (RBF) biosensors for guanidine, a common chaotropic agent that is a precursor to both fertilizer and explosive compounds. Guanidine is cell permeable and nontoxic to E. coli at millimolar concentrations, which in contrast to prior studies enabled direct activation of the riboswitch-based biosensor and corresponding reporter with ligand addition to cells. Our results reveal that the biosensors activate fluorescence in the cell within 4 min of guanidine treatment, which is at least 15 times faster than a reporter derived from the same riboswitch, and this rapid sensing activity is maintained for up to 1.6 weeks. Together, this study describes the design of two new biosensor topologies and showcases the advantages of RBF biosensors for monitoring dynamic processes in cell biology, biotechnology, and synthetic biology.
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Affiliation(s)
- Sudeshna Manna
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Johnny Truong
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
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48
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Abstract
Aptamers are single-stranded DNA or RNA molecules that can be identified through an iterative in vitro selection–amplification process. Among them, fluorogenic aptamers in response to small molecules have been of great interest in biosensing and bioimaging due to their rapid fluorescence turn-on signals with high target specificity and low background noise. In this review, we report recent advances in fluorogenic aptasensors and their applications to in vitro diagnosis and cellular imaging. These aptasensors modulated by small molecules have been implemented in different modalities that include duplex or molecular beacon-type aptasensors, aptazymes, and fluorogen-activating aptamer reporters. We highlight the working principles, target molecules, modifications, and performance characteristics of fluorogenic aptasensors, and discuss their potential roles in the field of biosensor and bioimaging with future directions and challenges.
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49
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Swetha P, Fan Z, Wang F, Jiang JH. Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing. J Mater Chem B 2021; 8:3382-3392. [PMID: 31984401 DOI: 10.1039/c9tb02668a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergence of genetically encoded light-up RNA aptamers has provided fascinating tools for studying intracellular small ligands and biomacromolecules owing to their high fluorescence activation degree and facile programmability. Here we review the burgeoning field of light-up RNA aptamers. We first briefly introduce light-up RNA aptamers with a focus on the photophysical properties of the fluorogens. Then design strategies of genetically encoded light-up RNA aptamer based sensors including turn-on, signal amplification and ratiometric rationales are emphasized.
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Affiliation(s)
- Puchakayala Swetha
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hu-nan University, Changsha, 410082, P. R. China.
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50
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Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Res 2021; 49:1784-1800. [PMID: 33469651 PMCID: PMC7897497 DOI: 10.1093/nar/gkaa1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Stefan Hammer
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, Inselstr. 22, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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