Multiscale Conformational Dynamics of DNA Holliday Junctions Modulated by Ion Concentration: Insights from...

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• DNA Holliday junctions (HJ) are critical intermediates in DNA repair and genetic recombination.
• Divalent cations, particularly Mg2+, are essential for stabilizing HJ structure.
• The precise role of Mg2+ in the single-molecule conformational dynamics of HJs is not fully understood.

Purpose of the Study:

• To investigate the effect of Mg2+ concentration on the microsecond-timescale conformational dynamics and diffusion of DNA Holliday junctions.
• To elucidate the physical principles governing HJ behavior during recombination.

Main Methods:

• Fluorescence Correlation Spectroscopy (FCS) was employed to measure conformational fluctuations and diffusion.
• Single-molecule time-resolved fluorescence anisotropy was used to assess rotational dynamics.
• Mean Squared Displacement (MSD) analysis was performed to evaluate molecular displacement.

Main Results:

• Increasing Mg2+ concentration induced three distinct dynamic modes in DNA HJs on the microsecond timescale.
• Mg2+ led to a 2.2-fold decrease in diffusion coefficient and a reduced hydrodynamic radius, indicating structural compaction.
• Anisotropy measurements ruled out Mg2+-induced oligomerization, and MSD analysis confirmed monomeric diffusion.

Conclusions:

• Mg2+ concentration directly influences the microsecond-scale dynamics and structural compactness of DNA Holliday junctions.
• This study provides fundamental insights into the physical behavior of recombination intermediates at the single-molecule level.
• The findings link ion-dependent structural changes to dynamic processes crucial for DNA metabolism.