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Related Concept Videos

Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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Microbial Biosensors01:17

Microbial Biosensors

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Microbial biosensors are analytical devices that utilize living microbes to detect specific substances through measurable signals. These devices consist of two main components: biosensing organisms and signal-transducing elements. Biosensing organisms, such as Escherichia coli or Saccharomyces cerevisiae, are typically housed in multiwell plates connected to transducers, enabling rapid, real-time detection of target analytes.Signal Generation MechanismWhen a target analyte—such as...
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Reporter Genes02:11

Reporter Genes

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Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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Updated: Mar 20, 2026

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues
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Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells.

J L Litke1, M You2, S R Jaffrey1

  • 1Tri-Institutional Chemical Biology Program at Weill-Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, NY, United States; Weill Medical College, Cornell University, New York, NY, United States.

Methods in Enzymology
|June 1, 2016
PubMed
Summary

We developed novel RNA-based sensors, Spinach riboswitches, that fluoresce when binding small molecules. This allows for live-cell imaging and measurement of various metabolites.

Keywords:
Cellular imagingDynamicsFluorescenceMetaboliteRNA probesRiboswitchSensor

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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Cell Biology

Background:

  • Genetically encoded small-molecule sensors are crucial for understanding cellular dynamics.
  • RNA-based sensors offer a promising avenue for real-time metabolite monitoring.
  • Naturally occurring riboswitches can be engineered into functional biosensors.

Purpose of the Study:

  • To describe the design and optimization of RNA-based sensors, specifically Spinach riboswitches.
  • To provide a method for characterizing these sensors in vitro and in vivo.
  • To enable live-cell imaging of metabolites using these novel sensors.

Main Methods:

  • Engineering RNA-based sensors by fusing natural riboswitches with the Spinach aptamer.
  • Optimizing sensor performance by adjusting critical RNA sequence elements.
  • In vitro characterization and bacterial expression for live-cell imaging applications.

Main Results:

  • Development of fluorogenic Spinach riboswitch sensors that exhibit fluorescence proportional to small-molecule binding.
  • Demonstration of a stepwise procedure for sensor design, optimization, and characterization.
  • Successful application of these sensors for live-cell imaging of metabolites in bacteria.

Conclusions:

  • Spinach riboswitch sensors provide a simple and versatile platform for fluorescence-based metabolite measurement.
  • These sensors are applicable to a wide range of analytes, including nucleotides, amino acids, and ions.
  • The described methods facilitate the development and application of RNA-based biosensors for cellular research.