Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations

Biophysical Journal

Volumn 75, Issue 6, 1998, Pages 3057-3063

  Hammermann, Markus ^a   Brun, Nathalie ^a   Kienin, Konstantin V ^a   May, Roland ^b   Tóth, Katalin ^a   Langowski, Jörg ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b INSTITUT LAUE LANGEVIN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; SODIUM CHLORIDE;

ARTICLE; CRYOELECTRON MICROSCOPY; DNA HELIX; MODEL; MOLECULAR DYNAMICS; NEUTRON SCATTERING; SYSTEM ANALYSIS;

EID: 0031793539     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77746-X     Document Type: Article

References (29)

1. Adrian, M., B. ten Heggeler-Bordier, W. Wahli, A. Z. Stasiak, A. Stasiak, and J. Dubochet. 1990. Direct visualization of supercoiled DNA molecules in solution. EMBO J. 9:4551-4554.
2. Bates A. D., and A. Maxwell. 1993. DNA Topology. Oxford University Press, Oxford.
3. Bednar, J., P. Furrer, A. Stasiak, J. Dubochet, E. H. Egelman, and A. D. Bates. 1994. The twist, writhe and overall shape of superhelical DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix: possible implications for DNA structure in vivo. J. Mol. Biol. 235:825-847.
4. Boles, T. C., J. H. White, and N. R. Cozzarelli. 1990. Structure of plectonemically supercoiled DNA. J. Mol. Biol. 213:931-951.
5. Brady, G. W., M. Satkowski, D. Foos, and C. J. Benham. 1987. Environmental influences on DNA superhelicity: the effect of ionic strength on superhelix conformation in solution. J. Mol. Biol. 195:185-191.
6. Debye, P. 1915. Ann. Physik. 28:809-823.
7. Gebe, J. A., S.A. Allison, J. B. Clendenning, and J. M. Schurr. 1995. Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs. Biophys. J. 68:619-633.
8. 2+ on the structures of supercoiled DNAs: comparison of simulations with experiments. J. Mol. Biol. 262:105-128.
9. Grassian, V., G. W. Brady, and C. J. Benham. 1983. X-ray conformational study of the DNA duplex in solution. Biopolymers. 22:1523-1543.
10. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
11. Hammermann, M., C. Steinmaier, H. Merlitz, U. Kapp, W. Waldeck, G. Chirico, and J. Langowski. 1997. Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics. Biophys. J. 73:2674-2687.
12. Kapp, U., and J. Langowski. 1992. Preparation of DNA topoisomers by RP-18 high performance liquid chromatography. Anal. Biochem. 206: 293-299.
13. Klenin, K., M. D. Frank-Kamenetskii, and J. Langowski. 1995. Modulation of intramolecular interactions in superhelical DNA by curved sequences. A Monte Carlo simulation study. Biophys. J. 68:81-88.
14. Kienin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA and other worm-like chain polyelectrolytes. Biophys. J. 74:780-788.
15. Klenin, K. V., A. V. Vologodskii, V. V. Anshelevich, V. Y. Klishko, A. M. Dykhne, and M. D. Frank-Kamenetskii. 1991. Computer simulation of DNA supercoiling. J. Mol. Biol. 217:413-419.
16. Kremer, W., K. Klenin, S. Diekmann, and J. Langowski. 1993. DNA curvature influences the internal motion of superhelical DNA. EMBO J. 12:44.07-4412.
17. Langowski, J. 1987. Salt effects on internal motions of superhelical and linear pUC8 DNA. Biophys. Chem. 27:263-271.
18. Langowski, J., G. Chirico, and U. Kapp. 1994. DNA supercoil dynamics studied by dynamic light scattering and Brownian dynamics simulations. In Structural Biology: The State of the Art. R. H. Sarma and M. H. Sarma, editors. Adenine Press, Schenectady, NY. 175-189.
19. Langowski, J., and U. Giesen. 1989. Configurational and dynamic properties of different length superhelical DNAs measured by dynamic light scattering. Biophys. Chem. 34:9-18.
20. Langowski, J., U. Giesen, and C. Lehmann. 1986. Dynamics of superhelical DNA studied by photon correlation spectroscopy. Biophys. Chem. 25:191-200.
21. Merlitz, H., K. Rippe, K. Klenin, and J. Langowski. 1998. Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys. J. 74:773-779.
22. 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270:125-138.
23. Rippe, K., N. Mücke, and J. Langowski. 1997b. Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution. Nucleic Acids Res. 25:1736-1744.
24. Rybenkov, V. V., A. V. Vologodskii, and N. R. Cozzarelli. 1997. The effect of ionic conditions on the conformations of supercoiled DNA. 1. Sedimentation analysis. J. Mol. Biol. 267:299-311.
25. Schellman, J. A., and D. Stigter. 1977. Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA. Biopolymers. 16:1415-1434.
26. Schurr, J. M. 1977. Theory of dynamic light scattering by polymers and gels. Chem. Phys. 30:243-247.
27. Schurr, J. M., B. S. Fujimoto, P. Wu, and L. Song. 1992. Fluorescence studies of nucleic acids: dynamics, rigidities and structures. In Topics in Fluorescence Spectroscopy. J. R. Lakowicz, editor. Plenum Press, New York. 137-229.
28. Stigter, D. 1977. Interactions of highly charged colloidal cylinders with applications to double stranded DNA. Biopolymers. 16:1435-1448.
29. Vologodskii, A. V., S. D. Levene, K. V. Klenin, M. D. Frank-Kamenetskii, and N. R. Cozzarelli. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227:1224-1243.