Transcription Factor Binding
3D diffusion + 1D sliding — finding a binding site in a sea of DNA
Simulation
Add TF Molecule
Clear All TFs
Mark Binding Site
Sliding diffusion:
0.5
3D diffusion:
1.0
Sequence specificity:
5
Statistics
TF molecules:
0
Bound:
0
Sliding:
0
3D diffusing:
0
Binding events:
0
Mean search:
—
steps
Theory
Berg-Winter-von Hippel 1981
Optimal search: mix of
3D diffusion + 1D sliding
kon ~10⁸–10¹⁰ M⁻¹s⁻¹
(faster than 3D diffusion)
Energy landscape:
Specific site: −ΔG deep
Non-specific: shallow
Sliding correlates ~50bp