Polymer properties of polythymine as revealed by translational diffusion.

Area of Science:

• Biophysics
• Polymer Physics

Background:

• Single-stranded DNA (ssDNA) is often modeled as a semiflexible or wormlike chain.
• Understanding ssDNA's diffusional properties is crucial for biophysical and polymer physics applications.

Purpose of the Study:

• To investigate the length dependence of diffusional properties of homogeneous ssDNA (polythymine).
• To determine the scaling of hydrodynamic radius (Rh) and persistence length (Lp) with ionic strength.
• To compare experimental results with molecular dynamics (MD) simulations.

Main Methods:

• Fluorescence correlation spectroscopy (FCS) to measure diffusional properties of polythymine ssDNA.
• Molecular dynamics (MD) simulations to determine polymer properties like end-to-end distance, radius of gyration (S), and persistence length (Lp).

Main Results:

• Hydrodynamic radius (Rh) scales with chain length via a power law (exponent 0.5–0.7) dependent on ionic strength.
• Persistence length (Lp) scales with ionic strength (I) as Lp ~ Im, with m=-0.22±0.01 for 100-residue polythymine.
• Excellent agreement between simulated radius of gyration (S) and experimental Rh at 100 mM NaCl indicates shielded electrostatic interactions in solution.
• Polythymine (>30 residues) behaves as a semiflexible polymer with an intrinsic persistence length of ~1.7 nm.

Conclusions:

• Experimental and simulation data provide a consistent description of ssDNA's physical properties.
• Electrostatic interactions are shielded at physiological ionic strengths, allowing for semiflexible polymer modeling.
• Results offer a benchmark for theoretical and simulation studies of polyelectrolyte behavior.