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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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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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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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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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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.
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Ribozymes02:47

Ribozymes

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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis.

Robb Welty1, Andreas Schmidt1, Nils G Walter2

  • 1Department of Chemistry, Single Molecule Analysis Group and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.

Methods in Molecular Biology (Clifton, N.J.)
|October 13, 2022
PubMed
Summary
This summary is machine-generated.

Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) reveals how riboswitches change shape to control gene expression. This method uses fluorescent probes to measure RNA conformational switching dynamics.

Keywords:
Bacterial gene regulationConformational dynamicsRNA foldingRiboswitchSingle molecule fluorescence microscopy

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Riboswitches are RNA regulatory elements controlling gene expression in bacteria.
  • Ligand binding induces conformational changes in riboswitches, altering mRNA structure.
  • Understanding these dynamic structural transitions is key to deciphering gene regulation.

Purpose of the Study:

  • To introduce and validate Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) as a method.
  • To probe RNA structural isomerization and conformational switching at the single-molecule level.
  • To gain mechanistic insights into riboswitch function.

Main Methods:

  • Utilizing fluorescently labeled DNA or RNA oligonucleotide probes.
  • Employing Total Internal Reflection Fluorescence Microscopy (TIRFM) for monitoring.
  • Analyzing binding/dissociation kinetics using spike train and burst detection.

Main Results:

  • SiM-KARTS enables quantitative analysis of RNA conformational dynamics.
  • The method elucidates rate constants for riboswitch isomerization.
  • Demonstrated ability to study structural switching in single mRNA molecules.

Conclusions:

  • SiM-KARTS provides a powerful tool for studying dynamic RNA structures.
  • This technique offers mechanistic insights into riboswitch-mediated gene regulation.
  • Enables detailed kinetic analysis of RNA conformational transitions.