Allosteric interactions in a birod model of DNA

Area of Science:

• Biophysics
• Molecular Biology
• Genetics

Background:

• Allosteric interactions between distant DNA-bound molecules are well-documented.
• A comprehensive theoretical understanding of DNA elasticity governing these interactions is lacking.

Purpose of the Study:

• To quantify allosteric interactions between two DNA-bound entities using a birod elasticity theory.
• To establish a theoretical framework for understanding DNA allostery.

Main Methods:

• Developed a birod model representing DNA as two interacting elastic strands connected by an elastic web (basepairs).
• Modeled local DNA deformations caused by bound molecules.
• Calculated the interaction energy between two DNA-bound proteins as a function of their separation.

Main Results:

• The displacement field from bound entities decays exponentially with distance.
• DNA-protein interaction energy decays exponentially and oscillates with DNA's double helix periodicity.
• Interaction decay length depends on DNA mechanical properties and GC content.

Conclusions:

• The birod model successfully quantifies allosteric interactions on DNA.
• The model provides a continuum elasticity framework for DNA allosteric interactions.
• Findings align with experimental observations and offer insights into DNA mechanics.