DNA bending and twisting properties of integration host factor determined by DNA cyclization

Plasmid

Volumn 43, Issue 1, 2000, Pages 73-84

  Teter, Bruce ^a,b   Goodman, Steven D ^a   Galas, David J ^a,c  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UCLA SFVP   (United States)

^c KECK GRADUATE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; CURVED DNA; DNA BINDING PROTEIN; INTEGRATION HOST FACTOR;

ANISOTROPY; ARTICLE; CYCLIZATION; DNA CONFORMATION; DNA STRUCTURE; DNA SUPERCOILING; ESCHERICHIA COLI; MOLECULAR RECOGNITION; NONHUMAN; PROTEIN DNA BINDING;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0033984269     PISSN: 0147619X     EISSN: None     Source Type: Journal    
DOI: 10.1006/plas.1999.1443     Document Type: Article

References (44)

1. Calladine C. R., Drew H. R. Understanding DNA. 1997;Academic Press, San Diego. p. 120-144.
2. Clendenning J. B., Schurr J. M. Circularization of small DNAs in the presence of ethidium: A theoretical analysis. Biopolymers. 34:1994;849-868.
3. Douc-Rasy S., Kolb A., Prunell A. Protein-induced unwinding of DNA: Measurement by gel electrophoresis of complexes with DNA minicircles. Application to restriction endonuclease EcoRI, catabolite gene activator protein, and lac repressor. Nucleic Acids Res. 17:1989;5173-5189.
4. Dripps D., Wartell R. M. DNA bending induced by the catabolite activator protein allows ring formation of a 144 bp DNA. J. Biomol. Struct. Stereodynam. 5:1987;1-13.
5. Echols H. Multiple DNA-protein interactions governing high-precision DNA transactions. Science. 233:1986;1050-1055.
6. Gamas P., Chandler M. G., Prentki P., Galas D. J. Escherichia coli integration host factor binds specifically to the ends of the insertion sequence IS1 and to its major insertion hot-spot in pBR322. J. Mol. Biol. 195:1987;261-272.
7. Goodman S. D., Nash H. A. Functional replacement of a protein-induced bend in a DNA recombination site. Nature. 341:1989;251-254.
8. Goodman S. D., Velten N. J., Gao Q., Robinson S., Segall A. M. In vitro selection of integration host factor binding sites. J. Bacteriol. 181:1999;3246-3255.
9. Goodrich J. A., Schwartz M. L., McClure W. R. Searching for and predicting the activity of sites for DNA binding proteins: Compilation and analysis of the binding sites for E. coli integration host factor (IHF). Nucleic Acids Res. 18:1990;4993-5000.
10. Hales L. M., Gumport R. I., Gardner J. F. Examining the contribution of a dA-dT element to the conformation of Escherichia coli integration host factor-DNA complexes. Nucleic Acids Res. 24:1996;1780-1786.
11. Huisman O., Reeada P. R., Signon L., Kleckner N. Mutational analysis of IS10's outside end. EMBO J. 8:1989;2101-2109.
12. Kahn J. D., Crothers D. M. Protein-induced bending and DNA cyclization. Proc. Natl. Acad. Sci. 89:1992;6343-6347.
13. Kim J., de Haan G., Nardulli A. M., Shapiro D. J. Prebending the estrogen response element destabilizes binding of the estrogen receptor DNA binding domain. Mol. Cell. Biol. 17:1997;3173-3180.
14. Kosturko L. D., Daub E., Murialdo H. The interaction of E. coli integration host factor and lambda cos DNA: Multiple complex formation and protein-induced bending. Nucleic Acids Res. 17:1989;317-334.
15. Kur J., Hasan N., Szybalski W. Physical and biological consequences of interactions between integration host factor (integration host factor) and coliphage lambda late pR′ and its mutants. Gene. 81:1989;1-15.
16. Law S. M., Bellomy G. R., Schlax P. J., Record M. T. Jr. In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo. J. Mol. Biol. 230:1993;161-173.
17. Lee D. K., Horikoshi M., Roeder R. G. Interaction of TFIID in the minor groove of the TATA element. Cell. 67:1991;1241-1250.
18. Maniatis T., Fritsch E. F., Sambrook J. Molecular Cloning, A Laboratory Manual. 1982;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
19. Marko J. F., Siggia E. D. Bending and twisting elasticity of DNA. Macromolecules. 27:1994;981-988.
20. Mengeritsky G., Goldenberg D., Mendelson I., Giladi H., Oppenheim A. B. Genetic and biochemical analysis of the integration host factor of Escherichia coli. J. Mol. Biol. 231:1993;646-657.
21. Moitoso de Vargas L., Kim S., Landy A. DNA looping generated by DNA bending protein integration host factor and the two domains of lambda integrase. Science. 244:1989;1457-1461.
22. Nash H. A. Integration and excision of bacteriophage λ: The mechanism of conservative site-specific recombination. Annu. Rev. Genet. 15:1981;143-167.
23. Nash H. A. Lin E. C. C., Simon Lynch A. Regulation of Gene Expression in Escherichia coli. 1996;149-179.
24. Peck L. J., Wang J. C. Sequence dependence of the helical repeat of DNA in solution. Nature. 292:1981;375-378.
25. Pil P. M., Chow C. S., Lippard S. J. High-mobility-group 1 protein mediates DNA bending as determined by ring closures. Proc. Natl. Acad. Sci. 90:1993;9465-9469.
26. Prentki P., Chandler M., Galas D. J. E. coli integration host factor bends the DNA at the ends of IS1 and in an insertion hotspot with multiple integration host factor binding sites. EMBO J. 8:1987a;2479-2487.
27. Prentki P., Gamas P., Galas D. J., Chandler M. Functions of the ends of IS1. DNA Replication and Recombination. 1987b;A. R. Liss. p. 719-734.
28. Rice P. A., Yang S., Mizuuchi K., Nash H. A. Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn. Cell. 87:1996;1295-1306.
29. Richet E., Abcarian P., Nash H. A. The interaction of recombination proteins with supercoiled DNA: Defining the role of supercoiling in lambda integrative recombination. Cell. 46:1986;1011-1021.
30. Segall A. M., Goodman S. D., Nash H. A. Architectural elements in nucleoprotein complexes: Interchangeability of specific and non-specific DNA binding proteins. EMBO J. 13:1994;4536-4548.
31. Shindo H., Kanke F., Miyake M., Matsumoto U., Shimizu M. The binding specificity and affinity of E. coli integration host factor (IHF) are influenced by the flexibility of flanking regions of its recognition sites. Biol. Pharm. Bull. 18:1995;1328-1334.
32. Shimizu M., Miyake M., Kanke F., Martsumoto U., Shindo H. Characterization of the binding of HU and IHF, homologous histone-like proteins of Escherichia coli, to curved and uncurved DNA. Biochim. Biophys. Acta. 1264:1995;330-336.
33. Shore D., Baldwin R. L. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170:1983a;957-981.
34. Shore D., Baldwin R. L. Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170:1983b;983-1007.
35. Shrader T. E., Crothers D. M. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA. 86:1989;7418-7422.
36. Shure M., Vinograd J. The number of superhelical turns in native virion SV40 DNA and Minicol DNA determined by the band counting method. Cell. 8:1976;215-226.
37. Snyder U. K., Thompson J. F., Landy A. Phasing of protein-induced DNA bends in a recombination complex. Nature. 341:1989;255-257.
38. 4 and by DNA cyclization studies. Biochemistry. 35:1996;10815-10827.
39. Teyssier C., Toulme F., Touzel J. P., Gervais A., Maurizot J. C., Culard F. Preferential binding of the archaebacterial histone-like MC1 protein to negatively supercoiled DNA minicircles. Biochemistry. 35:1996;7954-7958.
40. Thompson N. J. F., Waechter-Brulla D., Gumport R. I., Gardner J. F., Moitoso de Vargas L., Landy A. Mutation in an integration host factor-binding site: Effect on lambda site-specific recombination and regulatory implications. J. Bacteriol. 168:1986;1343-1351.
41. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: Applications to lambda site-specific recombination complexes. Nucleic Acids Res. 16:1988;9687-9705.
42. Tsai M.-M., Fu Y.-H. F., Deonier R. C. Intrinsic bends and integration host factor binding at F plasmid oriT. J. Bacteriol. 172:1990;4603-4609.
43. Wang S., Cosstick R., Gardner J. F., Gumport R. I. The specific binding of Escherichia coli integration host factor involves both major and minor grooves of DNA. Biochemistry. 34:1995;13082-13090.
44. Yang S., Nash H. A. Comparison of protein binding to DNA in vivo and in vitro: Defining an effective intracellular concentration. EMBO J. 14:1995;6292-6300.