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Related Concept Videos

Riboswitches01:56

Riboswitches

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...
Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

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...
Ribosome Profiling02:24

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

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Related Experiment Video

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Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Riboswitch conformations revealed by small-angle X-ray scattering.

Jan Lipfert1, Daniel Herschlag, Sebastian Doniach

  • 1Department of Physics, Stanford University, Stanford, CA 94305, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 22, 2009
PubMed
Summary

Small-angle X-ray scattering (SAXS) reveals how magnesium ions and glycine binding influence riboswitch RNA structure and folding. This method provides low-resolution models of RNA conformations under varying conditions.

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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Background:

  • Riboswitches are RNA molecules regulating gene expression via ligand-induced conformational changes.
  • RNA structure is critically dependent on cation-RNA interactions due to the negatively charged backbone.
  • Understanding these interactions is key to deciphering gene regulation mechanisms.

Purpose of the Study:

  • To demonstrate the utility of small-angle X-ray scattering (SAXS) for probing RNA conformations.
  • To investigate the energetic coupling between magnesium ion (Mg2+) dependent folding and ligand binding in a glycine riboswitch.
  • To generate low-resolution structural models of the riboswitch under various solution conditions.

Main Methods:

  • Small-angle X-ray scattering (SAXS) was employed to analyze RNA structure.
  • Thermodynamic modeling was used in conjunction with SAXS data.
  • Ab initio shape reconstruction algorithms were utilized to build structural models.

Main Results:

  • SAXS effectively probes RNA conformations influenced by ligand and ion concentrations.
  • Energetic coupling between Mg2+ dependent folding and glycine binding was quantified.
  • Low-resolution structural models of the riboswitch were successfully generated.

Conclusions:

  • SAXS is a valuable technique for studying cation and ligand effects on RNA structure.
  • The study elucidates the coupled folding and binding mechanisms in a glycine riboswitch.
  • This approach provides insights into riboswitch structural dynamics and function.