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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.
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Translational Regulation01:29

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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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Types of RNA01:23

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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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Types of RNA01:20

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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 regulating 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

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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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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Ligand-responsive RNA mechanical switches.

Mark A Boerneke1, Thomas Hermann

  • 1a Department of Chemistry and Biochemistry ; University of California, San Diego ; La Jolla , CA USA.

RNA Biology
|July 10, 2015
PubMed
Summary
This summary is machine-generated.

New RNA mechanical switches, discovered in viruses like Hepatitis C virus (HCV) and Seneca Valley virus (SVV), act as ligand-responsive modules. These switches are crucial for viral translation and offer potential for therapeutics and RNA nanostructures.

Keywords:
AEV, avian encephalomyelitis virusBDV, border disease virusBVDV, bovine viral diarrhea virusCSFV, classical swine fever virusDHV, Duck hepatitis virusDPV, duck picornavirusGBV, GB virusGPV, giraffe pestivirusHCV, hepatitis C virusIRESIRES, internal ribosome entry siteIVT, in vitro translationNPHV, non-primate hepacivirusRNA switchSPV, simian picornavirusSVV, Seneca Valley virusconformational switchhepatitis C virusriboswitch

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Area of Science:

  • Molecular Biology
  • Virology
  • Structural Biology

Background:

  • Ligand-responsive RNA mechanical switches are novel regulatory elements.
  • Distinct from metabolite-sensing riboswitches, they possess defined ligand-free and bound states.
  • Initially identified in Hepatitis C virus (HCV) internal ribosome entry sites (IRES), these motifs are conserved across various viral genomes.

Purpose of the Study:

  • To identify and characterize new ligand-responsive RNA mechanical switches.
  • To elucidate the conserved function and structural features of these switches in viral translation initiation.
  • To explore their potential applications in therapeutic development and RNA nanostructure engineering.

Main Methods:

  • Bioinformatic analysis for identifying novel RNA switch sequences.
  • Structural determination (e.g., crystal structure) of representative RNA switches.
  • Functional assays to assess ligand binding and translation regulation.

Main Results:

  • Discovery of 7 new RNA mechanical switches, expanding the known repertoire to 12 examples.
  • Demonstration of conserved function in viral translation initiation despite sequence and structural variations.
  • Identification of conserved ligand recognition mechanisms between distinct viral switches (e.g., HCV and Seneca Valley virus).

Conclusions:

  • Ligand-responsive RNA mechanical switches are a conserved class of viral regulatory elements.
  • These switches offer unique structural and functional properties for therapeutic targeting.
  • Their predictable conformational changes make them promising building blocks for RNA nanostructures.