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Macromolecular shape significantly impacts diffusion in crowded cellular environments. Cylindrical DNA dramatically slows tracer movement, unlike spherical particles, highlighting shape

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Area of Science:

  • Biophysics
  • Cellular Biology
  • Physical Chemistry

Background:

  • Cellular environments are crowded with macromolecules like proteins and nucleic acids.
  • This crowding reduces the mobility of molecules, a phenomenon primarily studied based on occupied volume.
  • The influence of macromolecular shape on diffusion has received less attention.

Purpose of the Study:

  • To investigate the effect of macromolecular shape, specifically cylindrical double-stranded DNA (dsDNA), on tracer diffusion.
  • To compare the impact of dsDNA shape versus spherical crowders on molecular mobility.
  • To elucidate the mechanisms behind shape-dependent diffusion in crowded systems.

Main Methods:

  • Utilizing fluorescence correlation spectroscopy (FCS) to experimentally measure tracer diffusion.
  • Employing Brownian dynamics (BD) simulations to model tracer-particle interactions and diffusion.
  • Analyzing the excluded volume and attractive interactions between tracers and crowders of different shapes.

Main Results:

  • Cylindrical dsDNA significantly reduces tracer diffusion, with a 60% slowdown at only 5% volume fraction.
  • Spherical crowders (Ficoll70) cause a 10% slowdown at 5% volume fraction, requiring 35% for a 60% reduction.
  • BD simulations indicate larger excluded volume and different attractive interactions contribute to dsDNA's effect.
  • Rotational diffusion of dsDNA is less impacted by crowder shape than its translational motion.

Conclusions:

  • Molecular diffusion in crowded systems depends on both occupied volume fraction and macromolecular shape.
  • The shape and interactions of crowding agents play a critical role in modulating molecular mobility.
  • These findings are crucial for understanding molecular dynamics within complex intracellular environments.