Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability

Journal of Molecular Biology

Volumn 286, Issue 5, 1999, Pages 1293-1301

  Anselmi, C ^a   Bocchinfuso, G ^a   De Santis, P ^a   Savino, M ^b   Scipioni, A ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b Pasteur Institute   (Italy)

Author keywords

Competitive nucleosome reconstitution; Nucleosome stability; Sequence dependent DNA curvature; Sequence dependent DNA elasticity; Statistical thermodynamics of DNA superstructures

Indexed keywords

CURVED DNA;

ARTICLE; DNA SEQUENCE; NUCLEOSOME; PRIORITY JOURNAL; THERMOSTABILITY;

EID: 0033548524     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2575     Document Type: Article

References (43)

1. Anselmi C., Bocchinfuso G., De Santis P., Fuà M., Scipioni A., Savino M. Statistical thermodynamic approach for evaluating the writhe transformations in circular DNAs. J. Phys. Chem. sect. B. 102:1998;5704-5714.
2. Berman H. M. Hydration of DNA: take 2. Curr. Opin. Struct. Biol. 4:1994;345-350.
3. Blank T. A., Becker P. B. The effect of nucleosome phasing sequences and DNA topology on nucleosome spacing. J. Mol. Biol. 260:1996;1-8.
4. Boffelli D., De Santis P., Palleschi A., Savino M. The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning. Biophys. Chem. 39:1991;127-136.
5. n. Gel electrophoresis and circular dichroism studies. Biochem. Int. 27:1992;891-901.
6. Cacchione S., Cerone M. A., Savino M. In vitro low propensity to form nucleosomes of four telomeric sequences. FEBS Letters. 400:1997;37-41.
7. Dal Cornò M., De Santis P., Sampaolese B., Savino M. DNA superstructural features and nucleosomal organization of the two centromeres of Kluyveromyces lactis chromosome 1 and Saccharomices cerevisiae chromosome 6. FEBS Letters. 431:1998;66-70.
8. De Santis P., Fuà M., Palleschi A., Savino M. Relationship between intrinsic and induced curvature in DNAs: theoretical prediction of nucleosome positioning. Biophys. Chem. 46:1993;193-204.
9. De Santis P., Fuà M., Savino M., Anselmi C., Bocchinfuso G. Sequence dependent circularization of DNAs: a physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending. J. Phys. Chem. 100:1996;9968-9976.
10. Drew H. R., Dickerson R. E. Structure of a B -DNA dodecamer. III. Geometry of hydration. J. Mol. Biol. 151:1981;535-556.
11. Drew H. R., Travers A. A. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186:1985;773-790.
12. Duan Y., Wilkosz P., Crowley M., Rosenberg J. M. Molecular dynamics simulation study of DNA dodecamer d(CGCAATTGCG) in solution: conformation and hydration. J. Mol. Biol. 272:1997;553-572.
13. Fitzgerald P. C., Simpson R. T. Effects of sequence alterations in a DNA segment containing the 5S RNA gene from Lytechinus variegatus on positioning of a nucleosome core particle in vitro. J. Biol. Chem. 260:1985;15318-15324.
14. Flaus A., Richmond T. J. Positioning and stability MMTV 3′ LTR sequences. J. Mol. Biol. 275:1998;427-441.
15. Flaus A., Luger K., Tan S., Richmond T. J. Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals. Proc. Natl Acad. Sci. USA. 93:1996;1370-1375.
16. Godde J. S., Wolffe A. P. Nucleosome assembly on CTG triplet repeats. J. Biol. Chem. 271:1996;15222-15229.
17. Godde J. S., Kass S. U., Hirst M. C., Wolffe A. P. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J. Biol. Chem. 271:1996;24325-24328.
18. Gotoh O., Tagashira Y. Stabilities of nearest-neighbor doublets in double helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers. 20:1981;1033-1042.
19. 2segments measured by NMR spectroscopy. Nucl. Acids Res. 24:1996;2911-2918.
20. Kornberg R. D. Structure of chromatin. Annu. Rev. Biochem. 46:1977;931-954.
21. Klug A., Rhodes D., Smith J., Finch T. J., Thomas J. O. A low resolution structure for the histone core of the nucleosome. Nature. 287:1980;509-516.
22. Lowary P. T., Widom J. New DNA sequence rules for high affinity binding to historic octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:1998;19-42.
23. Luger K., Mäder A. W., Richmond R. K., Sargent D. F., Richmond T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
24. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu. Rev. Biochem. 49:1980;1115-1156.
25. Meersseman G., Pennings S., Bradbury E. M. Mobile nucleosomes - a general behavior. EMBO J. 11:1992;2951-2959.
26. Ornstein R. L., Rein R., Breen D. L., Macelroy R. D. An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers. 17:1978;2341-2360.
27. Ramsay N. Deletion analysis of a DNA sequence that positions itself precisely on the nucleosome core. J. Mol. Biol. 189:1986;179-188.
28. Richmond T. J., Finch J. T., Rusliton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 Å resolution. Nature. 311:1984;532-537.
29. Robinson C. R., Sligar S. G. Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Proc. Natl Acad. Sci. USA. 95:1998;2186-2191.
30. Rossetti L., Cacchione S., Fuà M., Savino M. Nucleosome assembly on telomeric sequences. Biochemistry. 37:1998;6727-6737.
31. Satchwell S., Drew H. R., Travers A. A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:1986;659-675.
32. Shrader T. E., Crothers D. M. Artificial nucleosome positioning sequences. Proc. Natl Acad. Sci. USA. 86:1989;7418-7422.
33. Shrader T. E., Crothers D. M. Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216:1990;69-84.
34. Shui X., McFail-Isom L., Hu G. G., Williams L. D. The B -DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry. 37:1998;8341-8355.
35. Spiegel M. R. Fourier Analysis. 1974;McGraw-Hill Book Co. New York.
36. Sprous D., Zacharias W., Wood Z. A., Harvey S. C. Dehydrating agents sharply reduce curvature in DNAs containing A tracts. Nucl. Acids Res. 23:1995;1816-1821.
37. Teplukhin A. V., Poltev V. I., Chuprina V. P. Dependence of the hydration shell structure in the minor groove of the DNA double helix on the groove width as revealed by Monte Carlo simulation. Biopolymers. 31:1991;1445-1453.
38. Travers A. A., Klug A. The bending of DNA in nucleosomes and its wider implications. Phil. Trans. Roy. Soc. London. 317:1987;537-561.
39. van Holde K. E. The nucleosome. Rich A. Chromatin. 1988;213-276 Springer-Verlag, New York.
40. nmotif. a common DNA repeat that excludes nucleosomes. Proc. Natl Acad. Sci. USA. 93:1996;8863-8867.
41. Wang Y., Gellibolian R., Shimizu M., Wells R. D., Griffith J. Long CCG triplet repeat blocks exclude nucleosomes: a possible mechanism for the nature of fragile sites in chromosomes. J. Mol. Biol. 263:1996;511-516.
42. Widlund H. R., Cao H., Simonsson S., Magnusson E., Simonsson T., Nielsen P. E., Kahn J. D., Crothers D. M., Kubista M. Identification and characterization of genomic nucleosome-positioning sequences. J. Mol. Biol. 267:1997;807-817.
43. Widom J. Toward a unified model of chromatin folding. Annu. Rev. Biophys. Chem. 18:1989;365-395.