Kinetics of site-site interactions in supercoiled DNA with bent sequences

Journal of Molecular Biology

Volumn 322, Issue 4, 2002, Pages 707-718

  Bussiek, Malte ^a   Klenin, Konstantin ^a   Langowski, Jörg ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Biotin streptavidin; DNA curvature; DNA looping; Kinetics; Supercoiled DNA

Indexed keywords

BIOTIN; CURVED DNA; OLIGONUCLEOTIDE; STREPTAVIDIN;

ARTICLE; BIOTINYLATION; CONTROLLED STUDY; DEVICE; DNA CROSS LINKING; DNA SEQUENCE; DNA SUPERCOILING; KINETICS; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; SCANNING FORCE MICROSCOPY; THEORY;

EID: 0036392202     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00817-3     Document Type: Article

References (42)

1. Matthews, K. S. (1992). DNA looping. Microbiol. Rev. 56, 123-136.
2. Schleif, R. (1992). DNA looping. Annu. Rev. Biochem. 61, 199-223.
3. von Hippel, P. H., Rees, W. A., Rippe, K. & Wilson, K. S. (1996). Specificity mechanisms in the control of transcription. Biophys. Chem. 59, 231-246.
4. Bellomy, G. R. & Record, M. T., Jr (1990). Stable DNA loops in vivo and in vitro: roles in gene regulation at a distance and in biophysical characterization of DNA. Prog. Nucl. Acids Res. 39, 81-128.
5. Vologodskii, A. V., Levene, S. D., Klenin, K. V., Frank-Kamenetskii, M. & Cozzarelli, N. R. (1992). Conformational and thermodynamic properties of super-coiled DNA. J. Mol. Biol. 227, 1224-1243.
6. Sprous, D. & Harvey, S. C. (1996). Action at a distance in supercoiled DNA - effects of sequence on slither, branching, and intramolecular concentration. Biophys. J. 70, 1893-1908.
7. Jian, H., Schlick, T. & Vologodskii, A. (1998). Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition. J. Mol. Biol. 284, 287-296.
8. Klenin, K. V. & Langowski, J. (2001). Diffusion-controlled intrachain reactions of supercoiled DNA: Brownian dynamics simulations. Biophys. J. 80, 69-74.
9. Klenin, K. V. & Langowski, J. (2001). Kinetics of intrachain reactions of supercoiled DNA: theory and numerical modeling. J. Chem. Phys. 114, 5049-5060.
10. Hoover, T. R., Santero, E., Porter, S. & Kustu, S. (1990). The integration host factor stimulates interaction of RNA polymerase with NifA, the transcriptional activator for nitrogen fixation operons. Cell, 63, 11-22.
11. Molina-López, J. A., Govantes, F. & Santero, E. (1994). Geometry of the process of transcription activation at the σ54-dependent nifH promoter of Klebsiella pneumoniae. J. Biol. Chem. 269, 25419-25425.
12. Claverie, M. F. & Magasanik, B. (1992). Positive and negative effects of DNA bending on activation of transcription from a distant site. J. Mol. Biol. 227, 996-1008.
13. 54-dependent nifH promoter. J. Mol. Biol. 227, 602-620.
14. Goodman, S. D. & Nash, H. A. (1989). Functional replacement of a protein-induced bend in a DNA recombination site. Nature, 341, 251-254.
15. Pfannschmidt, C. & Langowski, J. (1998). Superhelix organization by DNA curvature as measured through site-specific labeling. J. Mol. Biol. 275, 601-611.
16. Laundon, C. H. & Griffith, J. D. (1988). Curved helix segments can uniquely orient the topology of super-twisted DNA. Cell, 52, 545-549.
17. Klenin, K. V., Frank-Kamenetskii, M. D. & Lan-gowski, J. (1995). Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. Biophys. J. 68, 81-88.
18. Chirico, G. & Langowski, J. (1996). Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys. J. 71, 955-971.
19. Kremer, W., Klenin, K., Diekmann, S. & Langowski, J. (1993). DNA curvature influences the internal motions of supercoiled DNA. EMBO J. 12, 4407-4412.
20. 54-holoenzyme. J. Mol. Biol. 300, 709-725.
21. Diekmann, S. (1987). Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucl. Acids Res. 15, 247-265.
22. Pfannschmidt, C., Schaper, A., Heim, G., Jovin, T. M. & Langowski, J. (1996). Sequence-specific labeling of superhelical DNA by triple helix formation and psor-alen crosslinking. Nucl. Acids Res. 24, 1702-1709.
23. Jacobson, H. & Stockmayer, W. H. (1950). Intramole-cular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 18, 1600-1606.
24. Rippe, K., von Hippel, P. H. & Langowski, J. (1995). Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20, 500-506.
25. Jones, M. L. & Kurzban, G. P. (1995). Noncooperativ-ity of biotin binding to tetrameric streptavidin. Biochemistry, 34, 11750-11756.
26. Keller, W. (1975). Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc. Natl Acad. Sci. USA, 72, 4876-4880.
27. Schätz, T. & Langowski, J. (1997). Curvature and sequence analysis of eukaryotic promoters. J. Biomol. Struct. Dynam. 15, 265-275.
28. Koo, H. S., Drak, J., Rice, J. A. & Crothers, D. M. (1990). Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry, 29, 4227-4234.
29. Ross, E. D., Den, R. B., Hardwidge, P. R. & Maher, I. L. (1999). Improved quantitation of DNA curvature using ligation ladders. Nucl. Acids Res. 27, 4135-4142.
30. Tóth, K., Sauermann, V. & Langowski, J. (1998). DNA curvature in solution measured by fluorescence resonance energy transfer. Biochemistry, 37, 8173-8179.
31. Lyamichev, V. I., Voloshin, O. N., Frank-Kamenetskii, M. D. & Soyfer, V. N. (1991). Photofootprinting of DNA triplexes. Nucl. Acids Res. 19, 1633-1638.
32. Rivetti, C., Walker, C. & Bustamante, C. (1998). Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J. Mol. Biol. 280, 41-59.
33. Mills, J. B., Vacano, E. & Hagerman, P. J. (1999). Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of Poly(dT) and Poly(dA). J. Mol. Biol. 285, 245-257.
34. Laue, T. M., Shah, B. D., Ridgeway, T. M. & Pelletier, S. L. (1992). Computer aided interpretation of analytical sedimentation data for proteins. In Analytical Ultracentrifugation in Biochemistry and Polymer Science (Harding, S. E., Rowe, A. J. & Horton, J. C., eds), pp. 90-125, Royal Society of Chemistry, Cambridge.
35. Huang, J., Schlick, T. & Vologodskii, A. (2001). Dynamics of site juxtaposition in supercoiled DNA. Proc. Natl Acad. Sci. USA, 98, 968-973.
36. Parker, C. N. & Halford, S. E. (1991). Dynamics of long-range interactions on DNA: the speed of synapsis during site-specific recombination by resolvase. Cell, 66, 781-791.
37. Oram, M., Marko, J. F. & Halford, S. E. (1997). Communications between distant sites on supercoiled DNA from non-exponential kinetics for DNA synapsis by resolvase. J. Mol. Biol. 270, 396-412.
38. Sessions, R. B., Oram, M., Szczelkun, M. D. & Half-ord, S. E. (1997). Random walk models for DNA synapsis by resolvase. J. Mol. Biol. 270, 413-425.
39. Hammermann, M., Brun, N., Klenin, K. V., May, R., Toth, K. & Langowski, J. (1998). Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations. Biophys. J. 75, 3057-3063.
40. Tsen, H. & Levene, S. D. (1997). Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method. Proc. Natl Acad. Sci. USA, 94, 2817-2822.
41. Kapp, U. & Langowski, J. (1992). Preparation of DNA topoisomers by RP-18 high-performance liquid chromatography. Anal. Biochem. 206, 293-299.
42. Bolshoy, A., McNamara, P., Harrington, R. E. & Trifonov, E. N. (1991). Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl Acad. Sci. USA, 88, 2312-2316.