ssDNA diffuses along replication protein A via a reptation mechanism

Area of Science:

• Molecular Biology
• Biophysics

Background:

• Replication protein A (RPA) is essential for eukaryotic DNA processing, interacting with single-stranded DNA (ssDNA).
• The RPA-ssDNA complex is increasingly recognized as a dynamic entity rather than a passive protector.

Purpose of the Study:

• To investigate the diffusion mechanism of ssDNA along RPA.
• To elucidate the role of aromatic and electrostatic interactions at the ssDNA-RPA interface.

Main Methods:

• Utilized a coarse-grained computational model to simulate RPA diffusion along a 60-nucleotide ssDNA strand.
• Modeled the ssDNA-RPA interface incorporating both aromatic and electrostatic interactions.

Main Results:

• Provided direct evidence for bulge formation during ssDNA diffusion along RPA.
• Identified that bulges store 1-7 nucleotides, and their dissolution drives ssDNA propagation, supporting the reptation mechanism.
• Observed increased cooperativity and diffusion coefficients with weaker aromatic interactions or homogenous electrostatic stabilization, potentially aligning with a sliding-without-bulge model.

Conclusions:

• The reptation mechanism, involving aromatic interactions and bulge formation, facilitates ssDNA mobility along RPA.
• Electrostatic interactions can promote ssDNA diffusion through bulge release, suggesting alternative models like sliding-without-bulge.
• Both interaction types are crucial for regulating ssDNA dynamics within the RPA complex.