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Related Concept Videos

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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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.
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Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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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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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
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Updated: Dec 13, 2025

Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis
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Receptor-based fluorescent sensors constructed from ribonucleopeptide.

Shun Nakano1, Hiroaki Konishi1, Takashi Morii1

  • 1Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.

Methods in Enzymology
|July 28, 2020
PubMed
Summary

Constructing fluorescent sensors for ligand detection is simplified using ribonucleopeptide (RNP) scaffolds. This method enhances sensor development by retaining receptor function and enabling simultaneous multi-ligand detection.

Keywords:
Diversity-oriented fluorophore libraryFluorescent sensorsIn vitro selectionModular designReceptorsRibonucleopeptideSimultaneous detection

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Sensor Technology

Background:

  • Receptor-based fluorescent sensors offer quantitative ligand detection but require laborious optimization.
  • Biomacromolecule receptors provide high substrate selectivity, yet sensor construction often diminishes receptor function.
  • Ribonucleopeptides (RNPs) present a promising scaffold to overcome these limitations in sensor development.

Purpose of the Study:

  • To introduce protocols for constructing fluorescent RNP sensors.
  • To demonstrate methods for retaining receptor affinity and selectivity in fluorescent sensors.
  • To explore the application of RNP sensors for simultaneous multi-ligand detection.

Main Methods:

  • In vitro selection of RNA-derived RNP libraries to identify specific receptors.
  • Modification of the RNP peptide N-terminus with fluorophores to create fluorescent sensors.
  • Structure-based modular design for RNP sensor construction.
  • Development of covalently linked RNP sensors for multiplexed detection.

Main Results:

  • Fluorescent RNP sensors can be constructed efficiently, retaining high affinity and selectivity for target ligands.
  • Protocols for both library selection and modular design enable robust sensor generation.
  • Covalently linked RNP sensors facilitate simultaneous detection of multiple ligands.

Conclusions:

  • Ribonucleopeptide scaffolds significantly streamline the development of functional fluorescent sensors.
  • The described methods provide a versatile platform for creating selective and sensitive RNP-based biosensors.
  • RNP sensors offer a powerful tool for advanced applications, including multiplexed analyte detection.