Intramolecular interference effects in dynamic light scattering: rigid double spirals and superhelical DNAs

Area of Science:

• Physics
• Biophysics
• Materials Science

Background:

• Dynamic light scattering (DLS) is a powerful technique for studying particle dynamics.
• Understanding the scattering from complex structures like double spirals is crucial for interpreting DLS data.
• Supercoiled DNA structures are fundamental in biological processes and their dynamics are of significant interest.

Purpose of the Study:

• To develop a theoretical framework for dynamic light scattering from rigid double spirals.
• To investigate the influence of geometrical interference effects on diffusion coefficients.
• To model the behavior of interwound supercoiled DNA and protein-DNA interactions.

Main Methods:

• A theoretical model treating the double spiral as a cylinder with helical scattering stripes was developed.
• The exact initial diffusion coefficient (Dapp(K)) was derived in terms of translational and rotational diffusion coefficients, dimensions, and pitch.
• The model was applied to analyze interference effects in supercoiled DNA and protein binding.

Main Results:

• Geometrical antiresonances between helical strands cause minima in the static structure factor (S(K)) and peaks in Dapp(K).
• These Dapp(K) peaks are sensitive to rotational dynamics around the symmetry axis.
• The model successfully explains experimental data for supercoiled DNA, including the effect of single-strand binding protein.

Conclusions:

• The developed theory accurately describes DLS from double spirals, highlighting the role of interference.
• The findings offer a new perspective on the dynamics of supercoiled DNA and how proteins interact with it.
• The theoretical predictions are in qualitative agreement with experimental observations for relaxed DNA dimers.