Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics
| Autor: | Markus Hammermann, Carola Steinmaier, Waldemar Waldeck, Holger Merlitz, Giuseppe Chirico, Jörg Langowski, Ulrike Kapp |
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| Rok vydání: | 1997 |
| Předmět: |
Models
Molecular Light Diffusion Biophysics Simian virus 40 Sodium Chloride Gyration Molecular physics Biophysical Phenomena Light scattering Scattering Radiation Computer Simulation Aqueous solution DNA Superhelical Chemistry Scattering Lasers Dynamic structure factor Relaxation (NMR) Crystallography DNA Viral Brownian dynamics Nucleic Acid Conformation Research Article Plasmids |
| Zdroj: | Biophysical Journal. 73(5):2674-2687 |
| ISSN: | 0006-3495 |
| DOI: | 10.1016/s0006-3495(97)78296-1 |
| Popis: | Using laser light scattering, we have measured the static and dynamic structure factor of two different superhelical DNAs, p1868 (1868 bp) and simian virus 40 (SV40) (5243 bp), in dilute aqueous solution at salt concentrations between 1 mM and 3 M NaCl. For both DNA molecules, Brownian dynamics (BD) simulations were also performed, using a previously described model. A Fourier mode decomposition procedure was used to compute theoretical light scattering autocorrelation functions (ACFs) from the BD trajectories. Both measured and computed autocorrelation functions were then subjected to the same multiexponential decomposition procedure. Simulated and measured relaxation times as a function of scattering angle were in very good agreement. Similarly, computed and measured static structure factors and radii of gyration agreed within experimental error. One main result of this study is that the amplitudes of the fast-relaxing component in the ACF show a peak at 1 M salt concentration. This nonmonotonic behavior might be caused by an initial increase in the amplitudes of internal motions due to diminishing long-range electrostatic repulsions, followed by a decrease at higher salt concentration due to a compaction of the structure. |
| Databáze: | OpenAIRE |
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