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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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Updated: Jul 15, 2025

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.

Hong Chen1, Yongping Xu1, Jianshi Jin2

  • 1State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.

Scientific Reports
|October 3, 2023
PubMed
Summary

KaScape is a new method to screen all DNA sequences for transcription factor (TF) binding. This high-throughput approach comprehensively maps TF binding landscapes, revealing moderate and low-affinity sites.

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Last Updated: Jul 15, 2025

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Exhaustively screening all possible DNA binding sequences for transcription factors (TFs) is challenging.
  • Understanding TF binding specificity is crucial for gene regulation studies.

Purpose of the Study:

  • To develop a high-throughput, exhaustive method for characterizing the binding affinity landscape of transcription factors.
  • To quantitatively assess the relative binding strength of TFs across all possible DNA sequences.

Main Methods:

  • Developed the KaScape method using randomized oligo synthesis to create a DNA pool with all possible sequences.
  • Separated bound from unbound double-stranded DNAs (dsDNAs) and sequenced them using next-generation sequencing.
  • Created 3D KaScape viewing software based on K-mer graphs to visualize binding affinities.

Main Results:

  • Applied KaScape to 12 plant AtWRKY proteins, revealing consistent binding to the core GAC sequence.
  • Identified binding sequences beyond the consensus W-box, including those with weak affinity.
  • Demonstrated KaScape's ability to detect moderate- and low-affinity binding sites.

Conclusions:

  • KaScape offers a sensitive, exhaustive, and easy-to-operate method for TF binding analysis.
  • The method comprehensively characterizes TF specificity and affinity landscapes.
  • KaScape is particularly valuable for identifying weak TF binding interactions.