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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Types of RNA01:23

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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Riboswitches01:56

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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

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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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Related Experiment Video

Updated: Aug 11, 2025

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
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Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity.

Xuan Ye1,2, Wen Yang3,4, Soon Yi1,2

  • 1Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.

Nature Communications
|February 9, 2023
PubMed
Summary
This summary is machine-generated.

The RNA Recognition Motif of RbFox protein achieves high sequence specificity through two distinct binding modes. These modes, involving structural changes, explain how RbFox selectively binds RNA targets.

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Related Experiment Videos

Last Updated: Aug 11, 2025

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

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Published on: September 30, 2016

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • RNA-binding proteins (RBPs) exhibit variable sequence specificity.
  • Mechanisms underlying high sequence specificity in some RBPs remain unclear.

Purpose of the Study:

  • To investigate how the RNA Recognition Motif (RRM) of RbFox achieves extraordinary RNA sequence specificity.
  • To elucidate the binding modes employed by RbFox and their structural basis.

Main Methods:

  • Affinity measurements of RbFox for various binding site variants.
  • Nuclear Magnetic Resonance (NMR) spectroscopy to study structural differences.

Main Results:

  • Identified two distinct binding modes for RbFox.
  • The first mode binds cognate and related RNAs with high affinity.
  • The second mode binds non-cognate RNAs with reduced affinity via thermodynamic penalties and involves significant conformational changes distant from the RNA-binding site.

Conclusions:

  • Distinct binding modes explain RbFox's extraordinary sequence selectivity.
  • Reveals a new layer of functional diversity, cross-talk, and regulation in RNA-protein interactions.