Polymer properties of polythymine as revealed by translational diffusion

Doose S, Barsch H, Sauer M (2007)
Biophysical Journal 93(4): 1224-1234.

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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 Rh scales according to a power law, with an exponent between 0.5 and 0.7 depending on ionic strength I. With Rh being proportional to the square root of the persistence length L-p, we found that L-p approximate to l(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.
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Doose S, Barsch H, Sauer M. Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal. 2007;93(4):1224-1234.
Doose, S., Barsch, H., & Sauer, M. (2007). Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal, 93(4), 1224-1234. doi:10.1529/biophysj.107.107342
Doose, S., Barsch, H., and Sauer, M. (2007). Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal 93, 1224-1234.
Doose, S., Barsch, H., & Sauer, M., 2007. Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal, 93(4), p 1224-1234.
S. Doose, H. Barsch, and M. Sauer, “Polymer properties of polythymine as revealed by translational diffusion”, Biophysical Journal, vol. 93, 2007, pp. 1224-1234.
Doose, S., Barsch, H., Sauer, M.: Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal. 93, 1224-1234 (2007).
Doose, Sören, Barsch, Hannes, and Sauer, Markus. “Polymer properties of polythymine as revealed by translational diffusion”. Biophysical Journal 93.4 (2007): 1224-1234.
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