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Related Experiment Video

Updated: Feb 6, 2026

Analysis of AtHIRD11 Intrinsic Disorder and Binding Towards Metal Ions by Capillary Gel Electrophoresis and Affinity Capillary Electrophoresis
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Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.

Tim Zeiske1, Nithya Baburajendran1, Anna Kaczynska1

  • 1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.

Cell Reports
|August 30, 2018
PubMed
Summary

Differences in DNA shape, not protein-DNA structure, explain varying transcription factor binding affinities. Intrinsic DNA shape influences protein binding, impacting gene regulation.

Keywords:
DNA binding specificityDNA shapeExtradenticleHox proteinsPbxabdominal Bcooperative bindinghomeodomainlow-affinity binding sites

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • Transcription factors (TFs) exhibit diverse binding affinities to DNA sequences.
  • Understanding how DNA sequence variations encode TF binding affinity is crucial for gene regulation studies.

Purpose of the Study:

  • To investigate the structural basis of varying affinities between Hox protein heterodimers and their DNA targets.
  • To elucidate the role of intrinsic DNA shape in modulating TF-DNA binding affinity.

Main Methods:

  • X-ray crystallography was used to determine the structures of four AbdominalB-Extradenticle heterodimer-DNA complexes.
  • Computational methods were employed to predict intrinsic DNA shapes.

Main Results:

  • Despite a ~20-fold difference in binding affinity, the overall structures of the four TF-DNA complexes were highly similar.
  • Intrinsic DNA shapes, predicted in the absence of protein, varied significantly among the target sites.
  • Lower binding affinities correlated with DNA sites requiring conformational changes upon protein binding.

Conclusions:

  • Intrinsic DNA shape, rather than TF-DNA complex structure, is a key determinant of binding affinity.
  • DNA shape provides a robust mechanism for modulating TF binding affinity without altering essential protein-DNA interactions.