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Richmond, T. J., & Davey, C. A. (2003). The structure of DNA in the nucleosome core. Nature, 423(6936), 145–150.

Authors 2
  1. Timothy J. Richmond (first)
  2. Curt A. Davey (additional)
References 40 Referenced 1,067
  1. van Holde, K. E. in Chromatin (ed. Rich, A.) (Springer, New York, 1988) / Chromatin by KE van Holde (1988)
  2. Kornberg, R. D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285–294 (1999) (10.1016/S0092-8674(00)81958-3) / Cell by RD Kornberg (1999)
  3. Elgin, S. C. R. & Workman, J. L. (eds) Chromatin Structure and Gene Expression (Oxford Univ. Press, Oxford, 2000)
  4. Simpson, R. T. Nucleosome positioning: Occurrence, mechanisms, and functional consequences. Prog. Nucleic Acid Res. Mol. Biol. 40, 143–184 (1991) (10.1016/S0079-6603(08)60841-7) / Prog. Nucleic Acid Res. Mol. Biol. by RT Simpson (1991)
  5. Wolffe, A. P. & Kurumizaka, H. The nucleosome: A powerful regulator of transcription. Prog. Nucleic Acid Res. Mol. Biol. 61, 379–422 (1998) (10.1016/S0079-6603(08)60832-6) / Prog. Nucleic Acid Res. Mol. Biol. by AP Wolffe (1998)
  6. Wyrick, J. J. et al. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418–421 (1999) (10.1038/46567) / Nature by JJ Wyrick (1999)
  7. Luger, K., Maeder, 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, 251–260 (1997) (10.1038/38444) / Nature by K Luger (1997)
  8. Pryciak, P. M. & Varmus, H. E. Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection. Cell 69, 769–780 (1992) (10.1016/0092-8674(92)90289-O) / Cell by PM Pryciak (1992)
  9. Kornberg, R. D. & Lorch, Y. Chromatin structure and transcription. Annu. Rev. Cell Biol. 8, 563–587 (1992) (10.1146/annurev.cb.08.110192.003023) / Annu. Rev. Cell Biol. by RD Kornberg (1992)
  10. Shimizu, M., Roth, S. Y., Szent-Gyorgyi, C. & Simpson, R. T. Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J. 10, 3033–3041 (1991) (10.1002/j.1460-2075.1991.tb07854.x) / EMBO J. by M Shimizu (1991)
  11. Flaus, A. & Richmond, T. J. Positioning and stability of nucleosomes on MMTV 3′LTR sequences. J. Mol. Biol. 275, 427–441 (1998) (10.1006/jmbi.1997.1464) / J. Mol. Biol. by A Flaus (1998)
  12. Meersseman, G., Pennings, S. & Bradbury, E. M. Mobile nucleosomes—a general behaviour. EMBO J. 11, 2951–2959 (1992) (10.1002/j.1460-2075.1992.tb05365.x) / EMBO J. by G Meersseman (1992)
  13. Polach, K. J. & Widom, J. Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation. J. Mol. Biol. 254, 130–149 (1995) (10.1006/jmbi.1995.0606) / J. Mol. Biol. by KJ Polach (1995)
  14. Studitsky, V. M., Kassavetis, G. A., Geiduschek, E. P. & Felsenfeld, G. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 278, 1960–1963 (1997) (10.1126/science.278.5345.1960) / Science by VM Studitsky (1997)
  15. Tsukiyama, T. The in vivo functions of ATP-dependent chromatin-remodelling factors. Nature Rev. Mol. Cell Biol. 3, 422–429 (2002) (10.1038/nrm828) / Nature Rev. Mol. Cell Biol. by T Tsukiyama (2002)
  16. Calladine, C. R. & Drew, H. R. Principles of sequence-dependent flexure of DNA. J. Mol. Biol. 192, 907–918 (1986) (10.1016/0022-2836(86)90036-7) / J. Mol. Biol. by CR Calladine (1986)
  17. Davey, C. A., Sargent, D. F., Luger, K., Maeder, A. W. & Richmond, T. J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319, 1097–1113 (2002) (10.1016/S0022-2836(02)00386-8) / J. Mol. Biol. by CA Davey (2002)
  18. Davey, C. A. & Richmond, T. J. DNA-dependent divalent cation binding in the nucleosome core particle. Proc. Natl Acad. Sci. USA 99, 11169–11175 (2002) (10.1073/pnas.172271399) / Proc. Natl Acad. Sci. USA by CA Davey (2002)
  19. Crick, F. H. C. & Klug, A. Kinky helix. Nature 255, 530–533 (1975) (10.1038/255530a0) / Nature by FHC Crick (1975)
  20. El Hassan, M. A. & Calladine, C. R. Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. R. Soc. Lond. A 355, 43–100 (1997) (10.1098/rsta.1997.0002) / Phil. Trans. R. Soc. Lond. A by MA El Hassan (1997)
  21. Lavery, R. & Sklenar, H. The definition of generalised helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6, 63–91 (1988) (10.1080/07391102.1988.10506483) / J. Biomol. Struct. Dynam. by R Lavery (1988)
  22. Young, M. A., Ravishanker, G., Beveridge, D. L. & Berman, H. M. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA–protein complexes. Biophys. J. 68, 2454–2468 (1995) (10.1016/S0006-3495(95)80427-3) / Biophys. J. by MA Young (1995)
  23. Olson, W. K. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6, 242–256 (1996) (10.1016/S0959-440X(96)80082-0) / Curr. Opin. Struct. Biol. by WK Olson (1996)
  24. Dickerson, R. E. DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906–1926 (1998) (10.1093/nar/26.8.1906) / Nucleic Acids Res. by RE Dickerson (1998)
  25. Goodsell, D. S. & Dickerson, R. E. Bending and curvature calculations in B-DNA. Nucleic Acids Res. 22, 5497–5503 (1994) (10.1093/nar/22.24.5497) / Nucleic Acids Res. by DS Goodsell (1994)
  26. El Hassan, M. A. & Calladine, C. R. Two distinct modes of protein-induced bending in DNA. J. Mol. Biol. 282, 331–343 (1998) (10.1006/jmbi.1998.1994) / J. Mol. Biol. by MA El Hassan (1998)
  27. Packer, M. J. & Hunter, C. A. Sequence–structure relationships in DNA oligomers: A computational approach. J. Am. Chem. Soc. 123, 7399–7406 (2001) (10.1021/ja003385u) / J. Am. Chem. Soc. by MJ Packer (2001)
  28. Yanagi, K., Prive, G. G. & Dickerson, R. E. Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 217, 201–214 (1991) (10.1016/0022-2836(91)90620-L) / J. Mol. Biol. by K Yanagi (1991)
  29. Shrader, T. E. & Crothers, D. M. Effects of DNA sequence and histone–histone interactions on nucleosome placement. J. Mol. Biol. 216, 69–84 (1990) (10.1016/S0022-2836(05)80061-0) / J. Mol. Biol. by TE Shrader (1990)
  30. Anselmi, C., Bocchinfuso, G., De Santis, P., Savino, M. & Scipioni, A. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J. Mol. Biol. 286, 1293–1301 (1999) (10.1006/jmbi.1998.2575) / J. Mol. Biol. by C Anselmi (1999)
  31. Dickerson, R. E. & Chiu, T. K. Helix bending as a factor in protein/DNA recognition. Biopolymers 44, 361–403 (1997) (10.1002/(SICI)1097-0282(1997)44:4<361::AID-BIP4>3.0.CO;2-X) / Biopolymers by RE Dickerson (1997)
  32. Packer, M. J. & Hunter, C. A. Sequence-dependent DNA structure: The role of the sugar-phosphate backbone. J. Mol. Biol. 280, 407–420 (1998) (10.1006/jmbi.1998.1865) / J. Mol. Biol. by MJ Packer (1998)
  33. Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J. Biol. Chem. 257, 14686–14707 (1982) (10.1016/S0021-9258(18)33335-0) / J. Biol. Chem. by AV Fratini (1982)
  34. Olson, W. K., Gorin, A. A., Lu, X. J., Hock, L. M. & Zhurkin, V. B. DNA sequence-dependent deformability deduced from protein–DNA crystal complexes. Proc. Natl Acad. Sci. USA 95, 11163–11168 (1998) (10.1073/pnas.95.19.11163) / Proc. Natl Acad. Sci. USA by WK Olson (1998)
  35. Travers, A. A. & Klug, A. The bending of DNA in nucleosomes and its wider implications. Phil. Trans. R. Soc. Lond. B 317, 537–561 (1987) (10.1098/rstb.1987.0080) / Phil. Trans. R. Soc. Lond. B by AA Travers (1987)
  36. Richmond, T. J. & Widom, J. in Chromatin Structure and Gene Expression (eds Elgin, S. C. R. & Workman, J. L.) 1–23 (Oxford Univ. Press, Oxford, 2000) / Chromatin Structure and Gene Expression by TJ Richmond (2000)
  37. Widom, J. Role of DNA sequence in nucleosome stability and dynamics. Q. Rev. Biophys. 34, 269–324 (2001) (10.1017/S0033583501003699) / Q. Rev. Biophys. by J Widom (2001)
  38. Zivanovic, Y., Goulet, I., Revet, B., Le Bret, M. & Prunell, A. Chromatin reconstitution on small DNA rings II. DNA supercoiling on the nucleosome. J. Mol. Biol. 200, 267–290 (1988) (10.1016/0022-2836(88)90239-2) / J. Mol. Biol. by Y Zivanovic (1988)
  39. Klug, A. & Lutter, L. C. The helical periodicity of DNA on the nucleosome. Nucleic Acids Res. 9, 4267–4283 (1981) (10.1093/nar/9.17.4267) / Nucleic Acids Res. by A Klug (1981)
  40. Arnott, S., Dover, S. D. & Wonacott, A. J. Least-squares refinement of the crystal and molecular structures of DNA and RNA from X-ray data and standard bond lengths and angles. Acta Crystallogr. B 25, 2192–2206 (1969) (10.1107/S0567740869005450) / Acta Crystallogr. B by S Arnott (1969)
Dates
Type When
Created 22 years, 3 months ago (May 7, 2003, 12:46 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 2:14 p.m.)
Indexed 1 day, 2 hours ago (Sept. 3, 2025, 6:43 a.m.)
Issued 22 years, 4 months ago (May 1, 2003)
Published 22 years, 4 months ago (May 1, 2003)
Published Print 22 years, 4 months ago (May 1, 2003)
Funders 0

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@article{Richmond_2003, title={The structure of DNA in the nucleosome core}, volume={423}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature01595}, DOI={10.1038/nature01595}, number={6936}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Richmond, Timothy J. and Davey, Curt A.}, year={2003}, month=may, pages={145–150} }