51
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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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52
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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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53
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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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54
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Liu LS, Wang F, Ge Y, Lo PK. Recent Developments in Aptasensors for Diagnostic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9329-9358. [PMID: 33155468 DOI: 10.1021/acsami.0c14788] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yonghe Ge
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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55
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Savage JC, Shinde P, Yao Y, Davare MA, Shinde U. A Broccoli aptamer chimera yields a fluorescent K + sensor spanning physiological concentrations. Chem Commun (Camb) 2021; 57:1344-1347. [PMID: 33432937 DOI: 10.1039/d0cc07042d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA aptamer Broccoli accepts 2'fluorinated (2'F) pyrimidine nucleotide incorporation without perturbation of structure or fluorescence in the presence of potassium and DFHBI. However, the modification decreases Broccoli's apparent affinity for K+ >30-fold. A chimera of Broccoli RNAs with mixed chemistries displays linear fluorescent gain spanning physiological K+ concentrations, yielding an effective RNA-based fluorescent K+ sensor.
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Affiliation(s)
- Jonathan C Savage
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.
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56
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Al Mazid MF, Shkel O, Kharkivska Y, Lee JS. Application of fluorescent turn-on aptamers in RNA studies. Mol Omics 2021; 17:483-491. [PMID: 34137415 DOI: 10.1039/d1mo00085c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an intermediate player between DNA transcription and protein translation. RNAs also interact with other macromolecules and metabolites and regulate their fate. The emerging number of RNA identifications expanded new areas of study to determine their applicability and functional analysis. Recently, extensive research has been focused on visualizing RNA in living biological samples and a method has been developed by the evolution of specific fluorophore-binding aptamers through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. Several promising fluorescent turn-on aptamers are currently available, and they can detect RNA-RNA, RNA-protein, ligand binding, small molecule, and metabolite interactions in vitro and under live-cell conditions. Here we review the currently available fluorescent turn-on aptamers and discuss their applicability for analyzing the fate of targeted RNAs in in vitro and in vivo systems.
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Affiliation(s)
| | - Olha Shkel
- Bio-Med Program KIST-School UST, Seoul, 02792, Republic of Korea
| | | | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
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57
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Imaging mRNA trafficking in living cells using fluorogenic proteins. Curr Opin Chem Biol 2020; 57:177-183. [PMID: 32829251 DOI: 10.1016/j.cbpa.2020.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023]
Abstract
mRNAs play key roles in regulating diverse cellular functions. In many cases, mRNAs exhibit distinct intracellular localizations that are necessary for the spatiotemporal control of protein expression in cells. Therefore, imaging the localization and dynamics of these mRNAs is crucial for understanding diverse aspects of cellular function. In this review, we summarize how mRNA imaging can be achieved using tethered fluorescent proteins and fluorogenic aptamers. We discuss 'fluorogenic proteins' and describe how these recently developed RNA-regulated fluorescent proteins simplify mRNA imaging experiments.
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58
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Braselmann E, Rathbun C, Richards EM, Palmer AE. Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells. Cell Chem Biol 2020; 27:891-903. [PMID: 32640188 PMCID: PMC7595133 DOI: 10.1016/j.chembiol.2020.06.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023]
Abstract
The central dogma teaches us that DNA makes RNA, which in turn makes proteins, the main building blocks of the cell. But this over simplified linear transmission of information overlooks the vast majority of the genome produces RNAs that do not encode proteins and the myriad ways that RNA regulates cellular functions. Historically, one of the challenges in illuminating RNA biology has been the lack of tools for visualizing RNA in live cells. But clever approaches for exploiting RNA binding proteins, in vitro RNA evolution, and chemical biology have resulted in significant advances in RNA visualization tools in recent years. This review provides an overview of current tools for tagging RNA with fluorescent probes and tracking their dynamics, localization andfunction in live mammalian cells.
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Affiliation(s)
- Esther Braselmann
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Colin Rathbun
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Erin M Richards
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Amy E Palmer
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA.
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59
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Li X, Mo L, Litke JL, Dey SK, Suter SR, Jaffrey SR. Imaging Intracellular S-Adenosyl Methionine Dynamics in Live Mammalian Cells with a Genetically Encoded Red Fluorescent RNA-Based Sensor. J Am Chem Soc 2020; 142:14117-14124. [PMID: 32698574 PMCID: PMC8158784 DOI: 10.1021/jacs.0c02931] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
To understand the role of intracellular metabolites in cellular processes, it is important to measure the dynamics and fluxes of small molecules in living cells. Although conventional metabolite sensors composed of fluorescent proteins have been made to detect some metabolites, an emerging approach is to use genetically encoded sensors composed of RNA. Because of the ability to rapidly generate metabolite-binding RNA aptamers, RNA-based sensors have the potential to be designed more readily than protein-based sensors. Numerous strategies have been developed to convert the green-fluorescent Spinach or Broccoli fluorogenic RNA aptamers into metabolite-regulated sensors. Nevertheless, red fluorescence is particularly desirable because of the low level of red background fluorescence in cells. However, the red fluorescent variant of the Broccoli aptamer, Red Broccoli, does not exhibit red fluorescence in cells when imaged with its cognate fluorophore. It is not known why Red Broccoli is fluorescent in vitro but not in live mammalian cells. Here, we develop a new fluorophore, OBI (3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime-1-benzoimidazole), which binds Red Broccoli with high affinity and makes Red Broccoli resistant to thermal unfolding. We show that OBI enables Red Broccoli to be readily detected in live mammalian cells. Furthermore, we show that Red Broccoli can be fused to a S-adenosyl methionine (SAM)-binding aptamer to generate a red fluorescent RNA-based sensor that enables imaging of SAM in live mammalian cells. These results reveal a red fluorescent fluorogenic aptamer that functions in mammalian cells and that can be readily developed into red fluorescent RNA-based sensors.
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Affiliation(s)
- Xing Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Liuting Mo
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Jacob L Litke
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Sourav Kumar Dey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Scott R Suter
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, United States
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60
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Ebrahimi SB, Samanta D, Mirkin CA. DNA-Based Nanostructures for Live-Cell Analysis. J Am Chem Soc 2020; 142:11343-11356. [DOI: 10.1021/jacs.0c04978] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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61
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Zhang H, Yang L, Zhu X, Wang Y, Yang H, Wang Z. A Rapid and Ultrasensitive Thrombin Biosensor Based on a Rationally Designed Trifunctional Protein. Adv Healthc Mater 2020; 9:e2000364. [PMID: 32406199 DOI: 10.1002/adhm.202000364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/26/2020] [Indexed: 12/12/2022]
Abstract
Rapid and sensitive detection of thrombin is imperative for the early diagnosis, prevention, and treatment of thrombin-related diseases. Here, an ultrasensitive and rapid thrombin biosensor is developed based on rationally designed trifunctional protein HTs, comprising three functional units, including a far-red fluorescent protein smURFP, hydrophobin HGFI, and a thrombin cleavage site (TCS). smURFP is used as a detection signal to eliminate any interference from the autofluorescence of sample matrix to increase detection sensitivity. HGFI serve as an adhesive unit to allow rapid immobilization of HTs on a multiwall plate. The TCS linking HGFI and smURFP function as a sensing element to recognize and detect thrombin. HTs immobilization is symmetrically optimized and characterized. Thrombin assay reveals the specific recognition of active thrombin in samples and the hydrolysis of the immobilized HTs, resulting in a decrease in the fluorescence intensity of the sample in a thrombin concentration-dependent manner. The limit of detection (LOD) is as low as 0.2 am in the serum. To the authors' knowledge, this is the lowest LOD ever reported for any thrombin biosensor. This study sheds light on the engineering of multifunctional proteins for biosensing.
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Affiliation(s)
- Huayue Zhang
- School of Life SciencesTianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresCollege of Precision Instrument and Opto‐Electronics EngineeringTianjin University Tianjin 300072 China
| | - Lu Yang
- School of Life SciencesTianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresCollege of Precision Instrument and Opto‐Electronics EngineeringTianjin University Tianjin 300072 China
| | - Xiaqing Zhu
- School of Life SciencesTianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresCollege of Precision Instrument and Opto‐Electronics EngineeringTianjin University Tianjin 300072 China
| | - Yanyan Wang
- School of Life SciencesTianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresCollege of Precision Instrument and Opto‐Electronics EngineeringTianjin University Tianjin 300072 China
| | - Haitao Yang
- School of Life SciencesTianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresCollege of Precision Instrument and Opto‐Electronics EngineeringTianjin University Tianjin 300072 China
- Center for Anti‐Infective Research & DevelopmentTianjin International Joint Academy of Biotechnology and Medicine Tianjin 300457 China
| | - Zefang Wang
- School of Life SciencesTianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresCollege of Precision Instrument and Opto‐Electronics EngineeringTianjin University Tianjin 300072 China
- Center for Anti‐Infective Research & DevelopmentTianjin International Joint Academy of Biotechnology and Medicine Tianjin 300457 China
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62
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Steinmetzger C, Bäuerlein C, Höbartner C. Supramolecular Fluorescence Resonance Energy Transfer in Nucleobase‐Modified Fluorogenic RNA Aptamers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Carmen Bäuerlein
- Institute of Organic ChemistryUniversity of Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic ChemistryUniversity of Würzburg Am Hubland 97074 Würzburg Germany
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63
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Steinmetzger C, Bäuerlein C, Höbartner C. Supramolecular Fluorescence Resonance Energy Transfer in Nucleobase-Modified Fluorogenic RNA Aptamers. Angew Chem Int Ed Engl 2020; 59:6760-6764. [PMID: 32052536 PMCID: PMC7187157 DOI: 10.1002/anie.201916707] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/11/2020] [Indexed: 12/14/2022]
Abstract
RNA aptamers form compact tertiary structures and bind their ligands in specific binding sites. Fluorescence-based strategies reveal information on structure and dynamics of RNA aptamers. Herein, we report the incorporation of the universal emissive nucleobase analog 4-cyanoindole into the fluorogenic RNA aptamer Chili, and its application as a donor for supramolecular FRET to the bound ligands DMHBI+ or DMHBO+ . The photophysical properties of the new nucleobase-ligand-FRET pair revealed structural restraints for the overall RNA aptamer organization and identified nucleotide positions suitable for FRET-based readout of ligand binding. This strategy is generally suitable for binding-site mapping and may also be applied for responsive aptamer devices.
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Affiliation(s)
| | - Carmen Bäuerlein
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Claudia Höbartner
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
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64
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Abstract
A key approach to investigating RNA species in live mammalian cells is the ability to label them with fluorescent tags and track their dynamics in the complex cellular environment. The growing appreciation for the diversity of RNAs in nature, especially the roles of small, non-coding RNAs for cell function, calls for development of orthogonal RNA tagging systems. We previously developed Riboglow, a new RNA tagging system that features modular elements and hence the possibility to customize features for each application of choice. Riboglow consists of an RNA tag that is genetically fused to the RNA of interest and a small molecule that binds the RNA tag and elicits a fluorescence light up signal. Here, we present an overview of the Riboglow platform and compare and contrast the system with existing RNA tagging systems. Two step by step protocols for implementation of RNA imaging with Riboglow in live mammalian cells are presented, with special emphasis on guidelines that drive choices for modular elements in the Riboglow platform. Such modular elements include the RNA tag sequence and size, the number of RNA tag repeats per tagged RNA, the fluorescent color of the probe, the identity of the chemical linker in the probe, and the concentration of the probe used in live cells. Together, Riboglow is a new RNA tagging platform that enables robust live cell imaging of RNA dynamics, and this detailed protocol and guidelines for implementation will enable broad usage of Riboglow.
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