Structure and dynamics of M13mp19 circular single-strand DNA: effects of ionic strength

Area of Science:

• Biophysics
• Molecular Biology
• Physical Chemistry

Background:

• M13mp19 viral circular single-strand DNA's structural dynamics are sensitive to environmental factors.
• Understanding DNA behavior in solution is crucial for molecular biology and biophysics.

Purpose of the Study:

• To investigate the effect of sodium chloride (NaCl) concentration on the structural and dynamic properties of M13mp19 viral circular single-strand DNA.
• To analyze changes in base stacking, stability, and diffusion coefficients with varying salt concentrations.

Main Methods:

• Dynamic and static light scattering experiments were performed on M13mp19 DNA across a 10,000-fold range of NaCl concentrations (100 microM to 1.0 M).
• Circular dichroism (CD) spectroscopy and optical melting experiments were used to assess base stacking and DNA stability.
• The Rouse-Zimm chain model was applied to interpret light scattering data and estimate model parameters.

Main Results:

• Increased NaCl concentration led to enhanced base stacking and stability, as indicated by melting curves and CD spectra.
• Dynamic light scattering revealed two decaying components corresponding to global translation and internal subunit motions.
• The diffusion coefficient of internal subunits (Dplat) decreased by nearly 22% with increasing salt concentration, while the center of mass diffusion coefficient (D0) and radius of gyration (RG) showed non-monotonic and moderate variations, respectively.
• Rouse-Zimm model analysis indicated decreased static flexibility and diffusive displacements of internal segments with higher salt concentrations.

Conclusions:

• NaCl concentration significantly impacts the structural stability and dynamics of M13mp19 viral circular single-strand DNA.
• The findings suggest that increased salt leads to a more compact and less flexible DNA structure.
• The study provides insights into polyelectrolyte behavior and DNA conformational changes in response to ionic strength.