DNA Mechanical Strain Steers Transcription Factor Recognition.

Area of Science:

• Molecular Biology
• Biophysics
• Genomics

Background:

• DNA recognition by transcription factors (TFs) is primarily studied through base sequence preferences.
• The role of DNA's mechanical properties and backbone continuity in TF binding is poorly understood.
• Existing methods lack comprehensive maps of how DNA mechanics influence TF recognition.

Purpose of the Study:

• To systematically map how DNA backbone mechanics and continuity affect transcription factor binding across diverse families.
• To understand the position-dependent impact of DNA mechanical perturbations on TF recognition.
• To investigate the interplay between DNA mechanics, sequence specificity, and repair factor accessibility.

Main Methods:

• Development and application of PIC-NIC, a high-throughput platform using site-specific backbone nicks to perturb DNA mechanics.
• Integration of PIC-NIC mapping with TF-DNA structural determination, binding kinetics, and molecular simulations.
• Analysis of genomic single-strand break and repair maps.

Main Results:

• PIC-NIC revealed position-dependent responses of TFs to DNA backbone disruption.
• Mechanically sensitive sites were identified where nicking significantly reshapes TF binding and sequence specificity.
• Sensitive sites often correlate with strain-adapted DNA conformations like Hoogsteen, whose relaxation impacts binding.
• TF binding at nicked DNA may affect local repair factor accessibility.

Conclusions:

• DNA backbone mechanics represent a critical, position-resolved layer of transcription factor recognition.
• Understanding DNA mechanics provides new insights into TF binding specificity and regulation.
• These findings have implications for DNA repair mechanisms and genome stability.