Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1981 Oct 10;9(19):4879–4893. doi: 10.1093/nar/9.19.4879

Conformation of DNA in chromatin reconstituted from poly [d(A-T)] and the core histones.

S Brahms, S K Brahmachari, N Angelier, J G Brahms
PMCID: PMC327486  PMID: 7312620

Abstract

Present results provide direct evidence of the nature of a conformational change in DNA when nucleosomes are formed from core histones and poly [d(A-T)]. First, we have found some features which have characteristic aspects of the A like conformation of DNA. Thus, an increased contribution due to a sugar conformation close to C3'-endo puckering is detected in the Raman spectra. In addition, the circular dichroism (C.D.) spectra of reconstituted chromatin with poly [d(A-T)] exhibits an increases intensity at about 262 nm. A second feature acquired by poly [d(A-T)] in nucleosome formation from core histones is related to the presence of a negative band at about 280 nm in the C.D.spectra. The nature of this change is correlated with a DNA conformation characterized by a decreased number of base pairs per turn (28,29). This indicates that these two features of reconstituted nucleosomes reflect the presence of two types of DNA conformations, which overall form is of the B type (22,36).

Full text

PDF
4879

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson P., Bauer W. Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry. 1978 Feb 21;17(4):594–601. doi: 10.1021/bi00597a006. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974 Sep 15;88(2):509–521. doi: 10.1016/0022-2836(74)90498-7. [DOI] [PubMed] [Google Scholar]
  3. BRAHMS J., MOMMAERTS W. F. A STUDY OF CONFORMATION OF NUCLEIC ACIDS IN SOLUTION BY MEANS OF CIRCULAR DICHROISM. J Mol Biol. 1964 Oct;10:73–88. doi: 10.1016/s0022-2836(64)80029-2. [DOI] [PubMed] [Google Scholar]
  4. Baase W. A., Johnson W. C., Jr Circular dichroism and DNA secondary structure. Nucleic Acids Res. 1979 Feb;6(2):797–814. doi: 10.1093/nar/6.2.797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brahms S., Brahms J. Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J Mol Biol. 1980 Apr;138(2):149–178. doi: 10.1016/0022-2836(80)90282-x. [DOI] [PubMed] [Google Scholar]
  6. Brahms S., Brahms J., Van Holde K. E. Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3453–3457. doi: 10.1073/pnas.73.10.3453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bryan P. N., Wright E. B., Hsie M. H., Olins A. L., Olins D. E. Physical properties of inner histone-DNA complexes. Nucleic Acids Res. 1978 Oct;5(10):3603–3617. doi: 10.1093/nar/5.10.3603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chambon P. Summary: the molecular biology of the eukaryotic genome is coming of age. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1209–1234. doi: 10.1101/sqb.1978.042.01.122. [DOI] [PubMed] [Google Scholar]
  9. Depew D. E., Wang J. C. Conformational fluctuations of DNA helix. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4275–4279. doi: 10.1073/pnas.72.11.4275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Finch J. T., Lutter L. C., Rhodes D., Brown R. S., Rushton B., Levitt M., Klug A. Structure of nucleosome core particles of chromatin. Nature. 1977 Sep 1;269(5623):29–36. doi: 10.1038/269029a0. [DOI] [PubMed] [Google Scholar]
  11. Germond J. E., Bellard M., Oudet P., Chambon P. Stability of nucleosomes in native and reconstituted chromatins. Nucleic Acids Res. 1976 Nov;3(11):3173–3192. doi: 10.1093/nar/3.11.3173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Germond J. E., Hirt B., Oudet P., Gross-Bellark M., Chambon P. Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A. 1975 May;72(5):1843–1847. doi: 10.1073/pnas.72.5.1843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Goodwin D. C., Brahms J. Form of DNA and the nature of interactions with proteins in chromatin. Nucleic Acids Res. 1978 Mar;5(3):835–850. doi: 10.1093/nar/5.3.835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Goodwin D. C., Vergne J., Brahms J., Defer N., Kruh J. Nucleosome structure: sites of interaction of proteins in the DNA grooves as determined by Raman scattering. Biochemistry. 1979 May 15;18(10):2057–2064. doi: 10.1021/bi00577a033. [DOI] [PubMed] [Google Scholar]
  15. Gray D. M., Edmondson S. P., Lang D., Vaughan M. The circular dichroism and X-ray diffraction of DNA condensed from ethanolic solutions. Nucleic Acids Res. 1979;6(6):2089–2107. doi: 10.1093/nar/6.6.2089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ivanov V. I., Minchenkova L. E., Minyat E. E., Frank-Kamenetskii M. D., Schyolkina A. K. The B to A transition of DNA in solution. J Mol Biol. 1974 Aug 25;87(4):817–833. doi: 10.1016/0022-2836(74)90086-2. [DOI] [PubMed] [Google Scholar]
  17. Jakobovits E. B., Bratosin S., Aloni Y. A nucleosome-free region in SV40 minichromosomes. Nature. 1980 May 22;285(5762):263–265. doi: 10.1038/285263a0. [DOI] [PubMed] [Google Scholar]
  18. Klug A., Rhodes D., Smith J., Finch J. T., Thomas J. O. A low resolution structure for the histone core of the nucleosome. Nature. 1980 Oct 9;287(5782):509–516. doi: 10.1038/287509a0. [DOI] [PubMed] [Google Scholar]
  19. Levitt M. How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proc Natl Acad Sci U S A. 1978 Feb;75(2):640–644. doi: 10.1073/pnas.75.2.640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  21. Miller O. L., Jr, Beatty B. R. Visualization of nucleolar genes. Science. 1969 May 23;164(3882):955–957. doi: 10.1126/science.164.3882.955. [DOI] [PubMed] [Google Scholar]
  22. Oudet P., Germond J. E., Sures M., Gallwitz D., Bellard M., Chambon P. Nucleosome structure I: all four histones, H2A, H2B, H3, and H4, are required to form a nucleosome, but an H3-H4 subnucleosomal particle is formed with H3-H4 alone. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):287–300. doi: 10.1101/sqb.1978.042.01.031. [DOI] [PubMed] [Google Scholar]
  23. Pilet J., Blicharski J., Brahms J. Conformations and structural transitions in polydeoxynucleotides. Biochemistry. 1975 May 6;14(9):1869–1876. doi: 10.1021/bi00680a011. [DOI] [PubMed] [Google Scholar]
  24. Prunell A., Kornberg R. D., Lutter L., Klug A., Levitt M., Crick F. H. Periodicity of deoxyribonuclease I digestion of chromatin. Science. 1979 May 25;204(4395):855–858. doi: 10.1126/science.441739. [DOI] [PubMed] [Google Scholar]
  25. Rhodes D., Klug A. Helical periodicity of DNA determined by enzyme digestion. Nature. 1980 Aug 7;286(5773):573–578. doi: 10.1038/286573a0. [DOI] [PubMed] [Google Scholar]
  26. Rhodes D. Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucleic Acids Res. 1979;6(5):1805–1816. doi: 10.1093/nar/6.5.1805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Saragosti S., Moyne G., Yaniv M. Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell. 1980 May;20(1):65–73. doi: 10.1016/0092-8674(80)90235-4. [DOI] [PubMed] [Google Scholar]
  28. Simon R. H., Felsenfeld G. A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res. 1979 Feb;6(2):689–696. doi: 10.1093/nar/6.2.689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Simpson R. T., Künzler P. Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucleic Acids Res. 1979 Apr;6(4):1387–1415. doi: 10.1093/nar/6.4.1387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Thoma F., Koller T., Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol. 1979 Nov;83(2 Pt 1):403–427. doi: 10.1083/jcb.83.2.403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Varshavsky A. J., Sundin O., Bohn M. A stretch of "late" SV40 viral DNA about 400 bp long which includes the origin of replication is specifically exposed in SV40 minichromosomes. Cell. 1979 Feb;16(2):453–466. doi: 10.1016/0092-8674(79)90021-7. [DOI] [PubMed] [Google Scholar]
  32. Wang J. C. Helical repeat of DNA in solution. Proc Natl Acad Sci U S A. 1979 Jan;76(1):200–203. doi: 10.1073/pnas.76.1.200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wang J. C. Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. J Mol Biol. 1969 Jul 14;43(1):25–39. doi: 10.1016/0022-2836(69)90076-x. [DOI] [PubMed] [Google Scholar]
  34. Wells R. D., Blakesley R. W., Hardies S. C., Horn G. T., Larson J. E., Selsing E., Burd J. F., Chan H. W., Dodgson J. B., Jensen K. F. The role of DNA structure in genetic regulation. CRC Crit Rev Biochem. 1977;4(3):305–340. doi: 10.3109/10409237709102561. [DOI] [PubMed] [Google Scholar]
  35. Zimmerman S. B., Pheiffer B. H. A direct demonstration that the ethanol-induced transition of DNA is between the A and B forms: an X-ray diffraction study. J Mol Biol. 1979 Dec 25;135(4):1023–1027. doi: 10.1016/0022-2836(79)90526-6. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES