Crowding induces complex ergodic diffusion and dynamic elongation of large DNA molecules

Area of Science:

• Biophysics
• Molecular Biology
• Cellular Dynamics

Background:

• Molecular crowding is prevalent in cells but its effect on large DNA is unclear.
• Understanding genome-sized DNA dynamics in crowded environments is crucial for cell biology.

Purpose of the Study:

• To investigate the effects of molecular crowding on the mobility and conformation of genome-sized DNA.
• To determine the role of crowder size and concentration in DNA dynamics.

Main Methods:

• Tracking single, fluorescent-labeled large DNA molecules (11 and 115 kbp).
• Utilizing dextran solutions at varying concentrations (0-40%) to mimic intracellular crowding.
• Analyzing DNA diffusion, mobility, and conformational changes.

Main Results:

• DNA mobility reduction and elongation were observed under crowding conditions.
• Crowder size (10 kDa vs. 500 kDa dextran) significantly influenced DNA diffusion mechanisms and concentration dependence.
• 10-kDa dextran showed saturated effects, while 500-kDa dextran led to exponential mobility retardation and anomalous subdiffusion.
• DNA molecules elongated into lower-entropy states, with fluctuations dependent on DNA and crowder size.

Conclusions:

• DNA elongation and initial mobility reduction are driven by depletion interactions.
• Subdiffusive dynamics and significant mobility retardation result from reduced mobility of larger crowders.
• Crowding effects on DNA are a complex interplay of entropy and crowder mobility, elucidating cellular crowding impacts.