DNA packaging in bacteriophage: is twist important?

Area of Science:

• Biophysics
• Computational Biology
• Molecular Biology

Background:

• Bacteriophage capsids package viral DNA through complex processes.
• Understanding DNA packaging is crucial for viral replication and gene therapy applications.
• The role of mechanical forces, like rotation, in DNA conformation during packaging is not fully understood.

Purpose of the Study:

• To investigate the impact of rotational forces on DNA conformation during bacteriophage capsid packaging using computer simulations.
• To compare the final packaged DNA structures resulting from feeding with and without end rotation.
• To analyze the influence of packaging conformation on subsequent DNA ejection dynamics.

Main Methods:

• Dynamic simulations of a polymer chain (representing DNA) into a spherical confinement (bacteriophage capsid).
• Two simulation scenarios: one with rotation of the chain end during feeding, and one without.
• Analysis of final packaged conformations, chain segment density, and layer formation.
• Simulations of DNA ejection with and without Brownian forces.

Main Results:

• Feeding DNA with end rotation resulted in a spool-like conformation, consistent with experimental data.
• Feeding DNA without rotation led to a folded conformation, deviating from the spool model.
• A layered structure of chain segments was observed, more pronounced with rotation.
• Frequent layer-to-layer jumps of the polymer chain occurred in both scenarios.
• Brownian forces were essential for complete DNA ejection in the absence of external forces.

Conclusions:

• Rotational forces significantly influence the final conformation of DNA packaged within bacteriophage capsids, favoring a spool-like structure.
• The observed layered structure and chain dynamics may affect DNA disentanglement during ejection.
• Brownian motion plays a critical role in the efficient ejection of packaged DNA.