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Updated: Aug 15, 2025
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Single-Molecule Förster Resonance Energy Transfer Methods for Real-Time Investigation of the Holliday Junction Resolution by GEN1
Published on: September 18, 2019
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Integration Host Factor Binds DNA Holliday Junctions.
Shawn H Lin1,2, Dacheng Zhao1,2, Vivian Deng1
1Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA.
International Journal of Molecular Sciences
|January 8, 2023
Summary
Integration host factor (IHF) binds DNA Holliday junctions with high affinity, stabilizing them in an open conformation. This protein interaction influences DNA repair and recombination dynamics.
Area of Science:
- Structural biology
- Molecular biology
- Biophysics
Background:
- Integration host factor (IHF) is a key protein regulating DNA processes like packaging and recombination.
- IHF typically recognizes a specific DNA sequence, inducing a significant bend.
- DNA Holliday junctions (HJs) are critical intermediates in DNA repair and recombination.
Purpose of the Study:
- To investigate the binding mechanism of IHF to DNA Holliday junctions.
- To determine how IHF affects the conformational dynamics of HJs.
- To elucidate the role of IHF in DNA repair and recombination pathways.
Main Methods:
- Ensemble and single-molecule Förster resonance energy transfer (smFRET).
- Stopped-flow kinetic experiments.
- Analysis of junction conformational dynamics and protein-bound states.
Main Results:
- IHF binds HJs with high affinity, independent of the consensus sequence, indicating a structure-based recognition.
- IHF binding shifts HJ populations towards the open conformation, facilitating branch migration.
- IHF binding alters junction dynamics, with concentration-dependent effects on transition rates and evidence of a dynamic, partially dissociated state.
Conclusions:
- IHF plays a significant role in DNA recombination and repair by stabilizing HJs in an open conformation.
- IHF's interaction with HJs is structure-dependent and influences their dynamic behavior.
- These findings suggest additional roles for IHF in viral DNA integration and bacterial biofilm stabilization.
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