Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics

Biophysical Journal

Volumn 73, Issue 5, 1997, Pages 2674-2687

  Hammermann, Markus ^a   Steinmaier, Carola ^b   Merlitz, Holger ^c   Kapp, Ulrike ^d   Waldeck, Waldemar ^a   Chirico, Giuseppe ^e   Langowski, Jörg ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b SAP RESEARCH   (Germany)

^c MAX PLANCK INSTITUT FÜR KERNPHYSIK   (Germany)

^d EUROPEAN MOLECULAR BIOLOGY LABORATORY   (France)

^e UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PLASMID DNA; SODIUM CHLORIDE; VIRUS DNA;

ARTICLE; CONTROLLED STUDY; DECOMPOSITION; DNA STRUCTURE; DNA SUPERCOILING; DYNAMICS; LIGHT SCATTERING; MOTION; NONHUMAN; SIMIAN VIRUS 40; SIMULATION;

EID: 0030844210     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78296-1     Document Type: Article

References (38)

1. Anderson. P., and W. Bauer. 1978. Supercoiling of closed circular DNA: dependence upon ion type and concentration. Biochemistry. 17: 594-601.
2. Baase. W. A., and W. C. J. Johnson. 1979. Circular dichroism and DNA secondary structure. Nucleic Acids Res. 6:797-814.
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. Berg, O. G. 1979. Dynamics of circular wormlikc chains. Biopolymers. 18:2861-2874.
5. Boles, T. C., J. H. White, and N. R. Cuzzarelli. 1990. Structure of plectonemically supercoiled DNA. J. Mol. Biol. 213:931-951.
6. Borowiec, J. A., I., Zhang, S. Sasse-Dwight, and J. D. Gralla. 1987. DNA supercoiling promotes formation of a bent repression loop in lac DNA. J. Mol. Biol. 196:101-111.
7. Chirico, G., and J. Langowski. 1992. Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm. Macromolecules. 25:769-775.
8. Chirico, G., and J. Langowski. 1994. Kinetics of DNA supercoiling studied by Brownian dynamics simulation, Biopolymers. 34:415-433.
9. Chirico, G., and J. Langowski. 1996. Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys. J. 71:955-971.
10. Doi, M. and S. F. Edwards. 1986. The Theory of Polymer Dynamics. Oxford University Press, Oxford.
11. 2+ on the structures of supercoiled DNAs: comparison of simulations with experiments. J. Mol. Biol. 262:105-128.
12. Gebe, J. A., and J. M. Schurr. 1993. Intramolecular interference effects in dynamic light-scattering from rigid rings. Biopolymers. 33:1757-1764.
13. Gull, S. F., and G. J. Daniell. 1978. Image reconstruction from incomplete and noisy data. Nature. 272:686-690.
14. Hagerman. P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
15. Kapp, U., and J. Langowski. 1992. Preparation of DNA topoisomers by RP-18 high performance liquid chromatography. Anal. Biochem. 206: 293-299.
16. 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.
17. Kratky, O., and G. Porod. 1949. Röntgenuntersuchung gelöster Faden- moleküle. Rec. Trav. Chim. 68:1106-1113.
18. Kremer, W., K. Kienin, S. Diekmann, and J. Langowski. 1993. DNA curvature influences the internal motion of superhelical DNA. EMBO J. 12:4407-4412.
19. Langowski, J. 1987. Salt effects on internal motions of superhelical und linear pUC8 DNA. Bipophys. Chem. 27:263-271.
20. Langowski, J. 1997. Modelling large DNA molecules: long-range interactions and regulation of transcription. In Nucleic Acids and Molecular Biology. Springer. Heidelberg.
21. Langowski, J., and R. Bryan. 1991. Maximum entropy analysis of photon correlation spectroscopy data using a Bayesian estimate for the regularization parameter. Macromolecules. 24:6346-6348.
22. Langowski, J., G. Chirico, and U. Kapp. 1994a. DNA supercoil dynamics studied by dynamic light scattering and Brownian dynamics simulations. In Structural Biology: The State of the Art. Adenine Press. Schenectady, NY. 175-189.
23. Langowski, J., und U. Giesen. 1989. Configurational and dynamic properties of different length superhelical DNAs measured by dynamic light scattering. Biophys. Chem. 34:9-18.
24. Langowski, J., U. Giesen, and C. Lehmann. 1986. Dynamics of superhelical DNA studied by photon correlation spectroscopy. Biophys. Chem. 25:191-200.
25. Langowski, J., U. Kapp, K. Kienin, and A. Vologodskii. 1994b. Solution structure and dynamics of DNA topoisomers. Dynamic light scattering studies and Monte Carlo simulations. Biopolymers. 34:639-646.
26. Langowski, J., W. K. Olson, S. C. Pedersen, I. Tobias, T. P. Westcott, and Y. Yang. 1996. DNA supercoiling. localized bending and thermal fluctuations. Trends Biochem. Sci. 21:50.
27. Laundon, C. H., and J. D. Griffith. 1988. Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell. 52:545-549.
28. Lewis, R., J. H. Huang, and P. Pecora. 1985. Rotational and translational motion of supercoiled plasmids in solution. Macromolecules. 18: 944-948.
29. Provencher, S. 1984. CONTIN V2 User's Manual. EMBL Technical Report. European Molecular Biology Laboratory, Heidelberg, Germany.
30. Richter, G. 1997. Elektrostatische Effekte auf die Struktur superhelikaler DNA. Diplomarbeit Fachbereich Chemie. Universität Hannover, Hannover, Germany.
31. Schurr, J. M. 1977. Theory of dynamic light scattering by polymers and gels. Chem. Phys. 30:243-247.
32. Skilling, J., and K. K. Bryan. 1984. Maximum entropy image reconstruction: general algorithm. Mon. Not. R. Astr. Soc. 211:111-124.
33. Soda, K. 1984. Theory of the dynamic light scattering properties for circular semiflexible chains in solution. Macromolecules. 17: 2365-2375.
34. Stigter, D. 1977. Interactions of highly charged colloidal cylinders with applications to double stranded DNA. Biopolymers. 16:1435-1448.
35. ten Heggeler-Bordier, B., W. Wahli, M. Adrian, A. Stasiak, and J. Dubochet. 1992. The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template. EMBO J. 11:667-672.
36. 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.
37. Waldeck, W., H. Zentgraf, and F. Rösl. 1988. Topoisomerase II inhibitors influence simian virus 40 chromatin structure in vivo accompanied with inhibition of replication, transcription and changes in DNA supercoiling. Oncology. 45:107-116.
38. Zhang, P. S., I. Tobias, and W. K. Olson. 1994. Computer simulation of protein-induced structural changes in closed circular DNA. J. Mol. Biol. 242:271-290.