Polymer properties of polythymine as revealed by translational diffusion

¹ Applied Laser Physics and Laser Spectroscopy, Bielefeld University

^* To whom correspondence should be addressed. E-mail: sdoose{at}physik.uni-bielefeld.de.

Submitted on February 21, 2007
Revised on April 11, 2007
Accepted on 12 April 2007

	Abstract

Biopolymers, such as single-stranded DNA (ssDNA), are often described as semiflexible polymers or worm-like 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 non-labeled polythymine derivatives. We found excellent agreement for the length dependences of simulated S and experimental R_h measured at 100 mM NaCl, revealing that electrostratic interactions are completely shielded in aqueous solution with such ionic strength. MD simulations further showed that polythymine with more than ~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 about 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.

Key Words: fluorescence correlation spectroscopy, molecular dynamics simulation, persistence length, polyelectrolyte, single-stranded DNA, translational diffusion constant

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