Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

Area of Science:

• Polymer physics
• Biophysics
• Structural biology

Background:

• The physics of strong polymer bending remains largely unexplained.
• Existing models often fail to unify weak and strong bending behaviors.
• Understanding polymer bending is crucial for various biological systems.

Purpose of the Study:

• To develop a general quantitative framework for polymer bending.
• To unify weak and strong bending regimes under a single physical principle.
• To explain the underlying mechanisms of strong bending in polymers like DNA.

Main Methods:

• Development of a general theoretical framework for polymer bending.
• Derivation of a simple equation for polymer loop energy.
• Utilizing atomistic simulations (Lennard-Jones interactions) to investigate DNA bending.

Main Results:

• A new framework describes polymer bending, unifying weak and strong regimes.
• In strong bending, polymer energy varies linearly with the bending angle.
• The theory accurately predicts DNA cyclization experiments, including counter-intuitive results for short DNA loops.

Conclusions:

• The proposed framework provides a unified understanding of polymer bending.
• Non-convexity in bending energy, driven by short-range interactions, explains the linear regime.
• The theory has broad applicability, including protein-DNA complexes and nucleosomes.