Polymer Properties of Polythymine as Revealed by Translational Diffusion

Abstract

Biopolymers, such as single-stranded DNA (ssDNA), are often described as semiflexible polymers or wormlike chains. We investigated the length dependence of diffusional properties of homogeneous ssDNA (polythymine) with up to 100 nucleotides using fluorescence correlation spectroscopy. We found that the hydrodynamic radius R h scales according to a power law, with an exponent between 0.5 and 0.7 depending on ionic strength I. With R h being proportional to the square root of the persistence length L p, we found that L p ≈ I m, with m = −0.22 ± 0.01 for polythymine with 100 residues. For comparison, we performed molecular dynamics (MD) simulations with a force field that accounts for short-range interactions in vacuum, and determined the characteristic polymer properties end-to-end distance R, radius of gyration S, and persistence length L p of various labeled and nonlabeled polythymine derivatives. We found excellent agreement for the length dependence of simulated S and experimental R h measured at 100 mM NaCl, revealing that electrostatic interactions are completely shielded in aqueous solution at such ionic strength. MD simulations further showed that polythymine with >∼30 residues can be described as a semiflexible polymer with negligible influence of the fluorescent label; and that static flexibility is limited by geometrical and steric constraints as expressed by an intrinsic persistence length of ∼1.7 nm. These results provide a benchmark for theories and MD simulations describing the influence of electrostatic interactions on polyelectrolyte properties, and thus help to develop a complete and accurate description of ssDNA.