Helical correlations in curved DNA condensates

Area of Science:

• Structural biology
• Biophysics
• Molecular dynamics

Background:

• DNA-DNA interactions are crucial for chromosome structure and sequence recognition in confined cellular environments.
• Theoretical models predict helical correlations between DNA double helices at close proximity, but experimental evidence is limited.
• These predicted helical correlations appear incompatible with DNA curvature, a common feature in dense DNA states.

Purpose of the Study:

• To experimentally investigate and characterize helical correlations in curved DNA condensates.
• To understand how these correlations influence the mesoscale shape and nanoscale conformation of DNA.
• To explore the interplay between helical correlations, curvature, and DNA organization in vitro.

Main Methods:

• Cryo-electron microscopy was used to analyze DNA toroids formed in vitro with a condensing agent.
• Helical correlations and their alignment (in-phase) were assessed across various ionic concentrations.
• The structural rearrangements within growing toroids, including nucleation and propagation, were examined.

Main Results:

• In-phase helix alignments are favored in curved DNA toroids across a range of ionic concentrations.
• DNA toroid assembly involves radial nucleation and circumferential propagation, leading to polygonal shapes.
• Curved DNA condensates exhibit alternating flat and highly curved regions, with a local decrease in helical pitch in high-curvature areas.

Conclusions:

• Helical correlations play a significant role in organizing DNA within curved condensates.
• These correlations influence both the mesoscale morphology of DNA assemblies and the nanoscale conformation of the DNA double helix.
• The findings provide experimental validation for predicted helical correlations and their impact on DNA structure.