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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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Types of RNA01:23

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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.
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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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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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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Related Experiment Video

Updated: Sep 22, 2025

Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Structural Changes in Aptamers are Essential for Synthetic Riboswitch Engineering.

Janis Hoetzel1, Beatrix Suess2

  • 1Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. Electronic address: https://www.twitter.com/J_Hoetzel.

Journal of Molecular Biology
|May 20, 2022
PubMed
Summary

Synthetic riboswitches combine sensing and execution in RNA. New selection methods are needed to identify aptamers with crucial structural switching and binding dynamics for engineering effective synthetic riboswitches.

Keywords:
SELEXaptamerconformational switchingregulationriboswitch

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Area of Science:

  • Synthetic biology
  • Molecular biology
  • RNA engineering

Background:

  • Synthetic riboswitches integrate sensing and execution within a single RNA molecule.
  • In vitro selection methods like SELEX can theoretically generate aptamers for any ligand.
  • Few SELEX-derived aptamers are utilized for synthetic riboswitch engineering due to inadequate selection criteria.

Purpose of the Study:

  • To explore the functional principles of synthetic riboswitches.
  • To identify key characteristics of regulatory active aptamers selected in vitro.
  • To propose improved in vitro selection strategies for aptamers suitable for synthetic riboswitch development.

Main Methods:

  • Review of functional principles of synthetic riboswitches.
  • Analysis of structural switching and binding dynamics of regulatory RNAs.
  • Integration of findings with existing in vitro selection methods.

Main Results:

  • Conventional SELEX inadequately selects for aptamer structural switching and binding dynamics.
  • These dynamic characteristics are crucial for regulatory activity in synthetic riboswitches.
  • A gap exists between in vitro selected aptamers and their suitability for riboswitch engineering.

Conclusions:

  • A combination of capture-SELEX and functional screening is proposed.
  • This integrated approach aims for more successful in vitro selection of aptamers.
  • The proposed method will enhance the engineering of synthetic riboswitches with improved regulatory functions.