G-quadruplex modulation by E. coli SSB: A comprehensive study on binding affinities and modes using single-molecule...

Area of Science:

• Molecular Biology
• Biophysics
• Genomics

Background:

• G-quadruplexes (GQs) are crucial guanine-rich DNA/RNA structures involved in genomic stability.
• E. coli GQs identified in intergenic regions suggest potential antimicrobial targets.
• E. coli single-stranded DNA binding protein (SSB) is vital for DNA replication and repair.

Purpose of the Study:

• To investigate the interaction between homo-tetrameric E. coli SSB and GQ-forming single-stranded DNA (ssDNA).
• To explore SSB's binding modes and the resulting structural alterations in GQ-ssDNA.
• To understand the biological significance of SSB-GQ interactions in E. coli.

Main Methods:

• Microscale Thermophoresis (MST) to assess protein-DNA binding affinity.
• Conventional spectroscopic techniques to monitor structural changes.
• Single-molecule Förster Resonance Energy Transfer (smFRET) to probe conformational dynamics.

Main Results:

• E. coli SSB exhibits multifaceted binding to various GQ-ssDNA sequences and lengths.
• SSB binding induces significant conformational changes in GQ-ssDNA structures.
• Detailed insights into the wrapping of homo-tetrameric SSB around GQ-ssDNA were obtained.

Conclusions:

• E. coli SSB interacts with G-quadruplexes through diverse binding modalities.
• These interactions lead to substantial structural rearrangements of GQ-ssDNA.
• Findings provide a deeper understanding of SSB's role in managing DNA G-quadruplexes.