Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors

Sun, Zhining; Nguyen, Tony; McAuliffe, Kathleen; You, Mingxu

doi:10.3390/nano9020233

Cited by 32 publications

(30 citation statements)

References 141 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Alternative design strategies have been proposed using natural riboswitches and circularly permutated molecules. However, since these sensors and their development are out of the scope of this chapter, the reader is redirected to some excellent recent reviews on the topic [127][128][129]. While for a long time the use of these sensors in mammalian cells was challenged by the short half-life of small RNAs in these cells, the recent development of the Tornado technology allows to express these sensors as highly stable circular RNAs [68].…”

Section: Detection Of Other Biological Molecules and Ionsmentioning

confidence: 99%

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

Ryckelynck

2020

Methods in Molecular Biology

View full text Add to dashboard Cite

The central role of RNA in living systems made it highly desirable to have non-invasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-e ce ec e ca ed e a bec e e ce b d e e ca e c dab e RNA ca ed-a a e. Ye , e development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications will be presented and discussed.

show abstract

Section: Detection Of Other Biological Molecules and Ionsmentioning

confidence: 99%

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

Ryckelynck

2020

Methods in Molecular Biology

View full text Add to dashboard Cite

show abstract

“…Although the basic concept of SELEX is the same, there are several experimental parameters that may affect the overall success for each target [49]. One of the crucial points is the design of the initial nucleic acid library [50]. Single-stranded DNA or RNA libraries can be chemically synthesized and amplified by polymerase chain reaction (PCR).…”

Section: Experimental Design Of Selexmentioning

confidence: 99%

A Bottom-Up Approach for Developing Aptasensors for Abused Drugs: Biosensors in Forensics

et al. 2019

View full text Add to dashboard Cite

Aptamer-based point-of-care (POC) diagnostics platforms may be of substantial benefit in forensic analysis as they provide rapid, sensitive, user-friendly, and selective analysis tools for detection. Aptasensors have not yet been adapted commercially. However, the significance of the applications of aptasensors in the literature exceeded their potential. Herein, in this review, a bottom-up approach is followed to describe the aptasensor development and application procedure, starting from the synthesis of the corresponding aptamer sequence for the selected analyte to creating a smart surface for the sensitive detection of the molecule of interest. Optical and electrochemical biosensing platforms, which are designed with aptamers as recognition molecules, detecting abused drugs are critically reviewed, and existing and possible applications of different designs are discussed. Several potential disciplines in which aptamer-based biosensing technology can be of greatest value, including forensic drug analysis and biological evidence, are then highlighted to encourage researchers to focus on developing aptasensors in these specific areas.

show abstract

“…Fluorogenic RNA aptamers, for example, Spinach or Broccoli, can bind and activate the fluorescence of dyes such as 3,5‐difluoro‐4‐hydroxybenzylidene‐1‐trifluoroethyl‐imidazolinone (DFHBI‐1T) . By fusing a target‐binding aptamer into Spinach/Broccoli, genetically encoded RNA‐based sensors have been developed for live‐cell imaging of metabolites, signaling molecules, proteins, and metal ions …”

Section: Figurementioning

confidence: 99%

Genetically Encoded Ratiometric RNA‐Based Sensors for Quantitative Imaging of Small Molecules in Living Cells

Mudiyanselage

Shafiei

et al. 2019

Angewandte Chemie

Self Cite

View full text Add to dashboard Cite

Precisely determining the intracellular concentrations of metabolites and signaling molecules is critical in studying cell biology.F luorogenic RNA-based sensors have emerged to detect various targets in living cells.H owever,i ti s still challenging to apply these genetically encoded sensors to quantify the cellular concentrations and distributions of targets. Herein, using apair of orthogonal fluorogenic RNAaptamers, DNB and Broccoli, we engineered amodular sensor system to apply the DNB-to-Broccoli fluorescence ratio to quantify the cell-to-cell variations of target concentrations.These ratiometric sensors can be broadly applied for live-cell imaging and quantification of metabolites,s ignaling molecules,a nd other synthetic compounds.Fluorescent probes that allow live-cell imaging of small molecules have enabled us to better understand cellular signaling and metabolite flux. Va rious fluorescent smallmolecule probes and genetically encoded fluorescent protein (FP)-based sensors have been developed to image metabolites and signaling molecules. [1] Thef unction of FP sensors requires at arget-binding domain that can both selectively recognize the target and result in sufficient conformational change to refold the FP or change the orientation between two FPs. [2] However,f or many physiologically important analytes,t hese adequate target-binding domains are not easily identified. Thelimited signal-to-noise ratio has further prevented their wide applications. [3] We and others have developed an ew class of genetically encoded sensors based on fluorogenic RNAa ptamers. [4] Aptamers are short single-stranded oligonucleotides that can bind to their targets with high affinity and specificity. [5] Fluorogenic RNAa ptamers,f or example,S pinach or Broccoli, can bind and activate the fluorescence of dyes such as 3,5-difluoro-4-hydroxybenzylidene-1-trifluoroethyl-imidazolinone (DFHBI-1T). [6] By fusing at arget-binding aptamer into Spinach/Broccoli, genetically encoded RNA-based sensors have been developed for live-cell imaging of metabolites, signaling molecules,proteins,a nd metal ions. [4,7] Almost all these fluorogenic RNAs ensors were developed based on aS pinach/Broccoli-dye complex (l ex /l em , approximately 480 nm/ 503 nm). With as ingle-wavelength readout, artifacts can easily arise from variations in the cellular RNAdistributions.F or quantitative and multiplexed imaging of cellular analytes, [8] it is critical to develop new RNAsensor pairs that have little spectra overlap and that can be orthogonally imaged.Here,w ed evelop ratiometric RNAs ensors to quantify the cellular concentrations and distributions of small molecules.T he sensor comprises Broccoli and ad initroaniline (DN)-binding aptamer,D NB. [6b,9] We have engineered novel red-colored RNAs ensors by fusing target-binding aptamers into DNB.U sing Broccoli as the reference,w ec an quantitatively image various small molecules in living cells.We first wondered if it is possible to develop DNB-based metabolite sensors.D initroaniline is ag eneral co...

show abstract

Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors

Cited by 32 publications

References 141 publications

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

A Bottom-Up Approach for Developing Aptasensors for Abused Drugs: Biosensors in Forensics

Genetically Encoded Ratiometric RNA‐Based Sensors for Quantitative Imaging of Small Molecules in Living Cells

Contact Info

Product

Resources

About