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Helical correlations in curved DNA condensates.

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DNA double helices exhibit helical correlations in curved condensates, influencing mesoscale shape and nanoscale conformation. This study experimentally documents these interactions in DNA toroids, revealing how they shape DNA organization.

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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.