Effect of DNA supercoiling on the geometry of holliday junctions

Biochemistry

Volumn 45, Issue 43, 2006, Pages 12998-13006

  Mikheikin, Andrey L ^a   Lushnikov, Alexander Y ^a   Lyubchenko, Yuri L ^a,b  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC FORCE MICROSCOPY; CONFORMATIONS; GENE TRANSFER; GEOMETRY; ISOMERS; MOLECULAR DYNAMICS; SOLUTIONS;

CRUCIFORMS; DIFFERENT SUPERHELICAL DENSITIES; HOLLIDAY JUNCTIONS; SUPERHELICAL DENSITIES;

DNA SEQUENCES;

BUFFER; CATION; PLASMID DNA;

AQUEOUS SOLUTION; ARTICLE; ATOMIC FORCE MICROSCOPY; DENSITY; DNA CONFORMATION; DNA CRUCIFORM; DNA FOLDING; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA SUPERCOILING; DYNAMICS; GENE CONTROL; GEOMETRY; HOLLIDAY JUNCTION; IONIC STRENGTH; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

DNA; DNA, CRUCIFORM; DNA, SUPERHELICAL; MICROSCOPY, ATOMIC FORCE; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION; PLASMIDS;

EID: 33751085651     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061002k     Document Type: Article

References (37)

1. Sinden, R. R. (1994) DNA Structure and Function, Academic Press, San Diego, CA.
2. Kornberg, A., and Baker, T. A. (1992) DNA Replication. 2nd ed., Freeman, New York.
3. Jin, R., Fernandez-Beros, M. E., and Novick, R. P. (1997) Why is the initiation nick site of an AT-rich rolling circle plasmid at the tip of a GC-rich cruciform? EMRO J. 16, 4456-4466.
4. Dai, X., Greizerstein, M. B., Nadas-Chinni, K., and Rothman-Denes, L. B. (1997) Supercoil-induced extrusion of a regulatory DNA hairpin, Proc. Natl. Acad. Sci. U.S.A. 94, 2174-2179.
5. Shlyakhtenko, L. S., Hsieh, P., Grigoriev, M., Potaman, V. N., Sinden, R. R., and Lyubchenko, V. L. (2000) A cruciform structural transition provides a molecular switch for chromosome structure and dynamics, J. Mol. Biol. 296, 1169-1173.
6. Lilley, D. M. (2000) Structures of helical junctions in nucleic acids, Q. Rev. Biophys. 33, 109-159.
7. Varga-Weisz, P., van Holde, K., and Zlatanova, J. (1993) Preferential binding of histone HI to four-way helical junction DNA, J. Biol. Chem. 268, 20699-20700.
8. Varga-Weisz, P., Zlatanova, J., Leuba, S. H., Schroth, G. P., and van Holde, K. (1994) Binding of histones H1 and H5 and their globular domains to four-way junction DNA, Proc. Natl. Acad. Sci. U.S.A. 91, 3525-3529.
9. West, K. L., and Austin, C. A. (1999) Human DNA topoisomerase IIβ binds and cleaves four-way junction DNA in vitro, Nucleic Acids Res. 27, 984-992.
10. Pohler, J., Norman, D. G., Bramham, J., Bianchi, M. E., and Lilley, D. M. (1998) HMG box proteins bind to four-way DNA junctions in their open conformation, EMBO J. 17, 817-826.
11. Kamashev, D., and Rouviere-Yaniv, J. (2000) The histone-like protein HU binds specifically to DNA recombination and repair intermediates, EMBO J. 19, 6527-6535.
12. Lee, S., Cavallo, L., and Griffith, J. (1997) Human p53 binds Holliday junctions strongly and facilitates their cleavage, J. Biol. Chem. 272, 7532-75397
13. Waldmann, T., Baack, M., Richter, N., and Gruss, C. (2003) Structure-specific binding of the proto-oncogene protein DEK to DNA, Nucleic Acids Res. 31, 7003-7010.
14. Khuu, P. A., Voth, A. R., Hays, F. A., and Ho, P. S. (2006) The stacked-X DNA Holliday junction and protein recognition, J. Mol. Recognit. 19, 234-242.
15. Zlatanova, J., and van Holde, K. (1998) Binding to four-way junction DNA: A common property of architectural proteins? FASEB J. 12, 421-431.
16. Hays, F. A., Watson, J., and Ho, P. S. (2003) Caution! DNA crossing: Crystal structures of Holliday junctions, J. Biol. Chem. 278, 49663-49666.
17. Clegg, R. M., Murchie, A. I., Zechel, A., Carlberg, C., Diekmann, S., and Lilley, D. M. (1992) Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction, Biochemistry 31, 4846-4856.
18. Joo, C., McKinney, S. A., Lilley, D. M., and Ha, T. (2004) Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy, J. Mol. Biol. 341, 739-751.
19. McKinney, S. A., Freeman, A. D., Lilley, D. M., and Ha, T. (2005) Observing spontaneous branch migration of Holliday junctions one step at a time, Proc. Natl. Acad. Sci. U.S.A. 102, 5715-5720.
20. Srinivasan, A. R., and Olson, W. K. (1994) Computer models of DNA four-way junctions, Biochemistry 33, 9389-9404.
21. Lu, M., Guo, Q., Seeman, N. C. and Kallenbach, N. R. (1991) Parallel and antiparallel Holliday junctions differ in structure and stability, J. Mol. Biol. 221, 1419-1432.
22. Oussatcheva, E. A., Pavlicek, J., Sankey, O. F., Sinden, R. R., Lyubchenko, Y. L., and Potaman, V. N. (2004) Influence of global DNA topology on cruciform Formation in supercoiled DNA, J. Mol. Biol. 338, 735-743.
23. Pavlicek, J. W., Oussatcheva, E. A., Sinden, R. R., Potaman, V. N., Sankey, O. F., and Lyubchenko, Y. L. (2004) Supercoiling-induced DNA bending, Biochemistry 43, 10664-10668.
24. Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (1998) Structure and dynamics of supercoil-stabilized DNA cruciforms, J. Mol. Biol. 280, 61-72.
25. Lushnikov, A. Y., Brown, B. A., II. Oussatcheva, E. A., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2004) Interaction of the Zα domain of human ADARI with a negatively supercoiled plasmid visualized by atomic force microscopy, Nucleic Acids Res. 32, 4704-4712.
26. Shlyakhlenko, L. S., Gall, A. A., Filonov, A., Cerovac, Z., Lushnikov, A., and Lyubchenko, Y. L. (2003) Silatrane-based surface chemistry For immobilization of DNA, protein-DNA complexes and other biological materials, Ultramicroscopy 97, 279-287.
27. Lushnikov, A. Y., Bogdanov, A., and Lyubchenko, Y. L. (2003) DNA recombination: Holliday junctions dynamics and branch migration, J. Biol. Chem. 278, 43130-43134.
28. Lushnikov, A. Y., Potaman, V. N., Oussatcheva, E. A., Sinden, R. R., and Lyubchenko, Y. L. (2006) DNA strand arrangement within the SfiI-DNA complex: Atomic force microscopy analysis, Biochemistry 45, 152-158.
29. Nollmann, M., Stark, W. M., and Byron, O. (2004) Low-resolution reconstruction of a synthetic DNA holliday junction, Biophys. J. 86, 3060-3069.
30. Panyutin, I. G., and Hsieh, P. (1994) The kinetics of spontaneous DNA branch migration, Proc. Natl. Acad. Sci. U.S.A. 91, 2021-2025.
31. Karymov, M., Daniel, D., Sankey, O. F., and Lyubchenko, Y. L. (2005) Holliday junction dynamics and branch migration: Single-molecule analysis, Proc. Natl. Acad. Sci. U.S.A. 102, 8186-8191.
32. Vologodskii, A. (1999) Online Biophysical Chemistry Textbook. Biophysical Society. Bethesda, MD.
33. Hohng, S., Joo, C., and Ha, T. (2004) Single-molecule three-color FRET, Biophys. J. 87, 1328-1337.
34. Lyubchenko, Y. L., and Shlyakhtenko, L. S. (1997) Visualization of supercoiled DNA with atomic force microscopy in situ, Proc. Natl. Acad. Sci. U.S.A. 94, 496-501.
35. Parsons, C. A., Stasiak, A., Bennett, R. J., and West, S. C. (1995) Structure of a multisubunit complex that promotes DNA branch migration, Nature 374, 375-378.
36. Hatfield, G. W., and Benham, C. J. (2002) DNA topology-mediated control of global gene expression in Escherichia coli, Annu. Rev. Genet. 36, 175-203.
37. Champoux, J. J. (2001) DNA topoisomerases: Structure, function, and mechanism, Annu. Rev. Biochem. 70, 369-413.