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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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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Cis-regulatory Sequences02:02

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Related Experiment Video

Updated: Jan 20, 2026

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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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins.

Ravinder Singh1

  • 1Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder; ravinder.singh@colorado.edu.

Journal of Visualized Experiments : Jove
|August 27, 2019
PubMed
Summary

Researchers developed a new method to find RNA-binding protein binding sites. This technique uses iterative selection and amplification to identify unknown binding sequences for gene regulation studies.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Gene regulation is crucial for cellular function, involving transcriptional, post-transcriptional, translational, and post-translational control.
  • Sequence-specific nucleic acid-binding proteins are key regulators of gene expression, but their binding sites are often unknown.
  • Characterizing these binding sites is essential for understanding gene regulation.

Purpose of the Study:

  • To present a novel approach for identifying previously unknown binding sites for RNA-binding proteins.
  • To enable the characterization of binding specificities for proteins lacking defined binding sequences.

Main Methods:

  • The method involves iterative selection and amplification of sequences from a randomized pool.
  • Key steps include transcription, protein binding, and amplification of bound sequences.
  • Enriched sequences are identified through sequencing, and binding is validated using in vitro assays.

Main Results:

  • The described approach successfully identifies preferred binding sites for RNA-binding proteins.
  • In vitro and in vivo functional assays can confirm the biological relevance of identified sites.
  • This method is applicable to any RNA-binding protein where bound/unbound RNA separation is possible.

Conclusions:

  • A robust method is established for discovering and characterizing novel RNA-binding protein binding sites.
  • This technique significantly advances the study of gene regulation by providing tools to identify regulatory elements.
  • The approach facilitates a deeper understanding of how RNA-binding proteins control gene expression.