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PMID: 272625 Published · ppublish English Journal Article

Possibility of nonkinked packing of DNA in chromatin.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 75 ·No. 1 ·1978-01-00 ·Pages 103-7

Sussman JL, Trifonov EN

Abstract

The idea that DNA in chromatin can be packed smoothly, without breaking of base-stacking interactions, has been explored by both energetical estimations and stereochemical model building. A model of deformed DNA is built that fits reasonably to the known dimensions of a nucleosome. The model has slightly changed torsion angles in the sugarphosphate moieties relative to B DNA, varying gradually along the chains. The angle between planes of adjacent base pairs varies between 1 and 7 degrees. This model of deformed DNA does not have any unusually close nonbonded contacts and is evidently not the only possible model of smooth packing of DNA in chromatin. An energetical estimation of the critical radius of curvature of a smoothly bent DNA molecule is made using approximate potential functions for different van der Waals contracts in the B DNA structure. The critical radius of curvature of the deformed DNA-axis is close to the radius of a nucleosome (similar to 50 A). The smooth packing is a good alternative to models of kinked folding of DNA in nucleosomes.

MeSH Terms
Chromatin/ultrastructure DNA Models, Structural Nucleic Acid Conformation Thermodynamics
Chemicals
Chromatin DNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Sussman J L
Trifonov E N
References (32)
32 references, click to expand
  1. The molecular configuration of deoxyribonucleic acid. III. X-ray diffraction study of the C form of the lithium salt.
    J Mol Biol. 1961 Oct;3:547-65 PMID: 14470668
  2. Supercoiling energy and nucleosome formation: the role of the arginine-rich histone kernel.
    Nucleic Acids Res. 1977;4(5):1159-81 PMID: 331250
  3. Secondary structural complementarity between DNA and proteins.
    Proc Natl Acad Sci U S A. 1977 Apr;74(4):1458-62 PMID: 266187
  4. Biochemical evidence of variability in the DNA repeat length in the chromatin of higher eukaryotes.
    Proc Natl Acad Sci U S A. 1976 Dec;73(12):4382-6 PMID: 826906
  5. A comparative X-ray diffraction and circular dichroism study of DNA compact particles formed in water-salt solutions, containing poly(ethylene glycol).
    Nucleic Acids Res. 1976 Sep;3(9):2353-66 PMID: 787935
  6. Organization of DNA in chromatin.
    Proc Natl Acad Sci U S A. 1976 Sep;73(9):3068-72 PMID: 1067602
  7. Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5' yields to 3')-thymidylate-(5') hydrate (pTpT), and a possible structural model for polythymidylate.
    J Mol Biol. 1976 Nov 15;107(4):601-21 PMID: 1003477
  8. A model for chromatin based upon two symmetrically paired half-nucleosomes.
    Cell. 1976 Nov;9(3):409-17 PMID: 991271
  9. The flexibility of low molecular weight double-stranded DNA as a function of length. I. Light scattering measurements and the estimation of persistence lengths from light scattering, sedimentation and viscosity.
    Biophys Chem. 1976 Sep;5(3):301-18 PMID: 987812
  10. Mode of DNA packing within bacteriophage heads.
    J Mol Biol. 1973 Aug 5;78(2):255-9 PMID: 4747629
  11. Experimental and theoretical aspects of protein folding.
    Adv Protein Chem. 1975;29:205-300 PMID: 237413
  12. Early and late helix-coil transitions in closed circular DNA. The number of superhelical turns in polyoma DNA.
    J Mol Biol. 1968 Apr 14;33(1):173-97 PMID: 4296518
  13. The study of DNA-RNA-polymerase complexes by kinetic formaldehyde method.
    Eur J Biochem. 1976 Apr 1;63(2):607-15 PMID: 770176
  14. 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):1843-7 PMID: 168578
  15. Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences.
    J Mol Biol. 1974 Sep 15;88(2):523-33 PMID: 4453006
  16. Chromatin structure: a repeating unit of histones and DNA.
    Science. 1974 May 24;184(4139):868-71 PMID: 4825889
  17. Optimised parameters for A-DNA and B-DNA.
    Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9 PMID: 5040245
  18. Melting of DNA: its study and application as a research method.
    Biopolymers. 1970 Nov;9(11):1253-306 PMID: 4922326
  19. Electron microscopy of DNA polymerase bound to DNA.
    J Mol Biol. 1971 Jan 28;55(2):209-14 PMID: 4926886
  20. The binding of RNA polymerase to DNA.
    J Mol Biol. 1966 Oct 28;21(1):83-114 PMID: 5338997
  21. Conformation of polypeptides and proteins.
    Adv Protein Chem. 1968;23:283-438 PMID: 4882249
  22. Kinky helix.
    Nature. 1975 Jun 12;255(5509):530-3 PMID: 1095931
  23. RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate.
    J Mol Biol. 1976 Jun 14;104(1):109-44 PMID: 957429
  24. The mass per unit length of chromatin by low-angle x-ray scattering.
    FEBS Lett. 1976 Apr 15;64(1):89-91 PMID: 1269768
  25. Compact form of DNA induced by spermidine.
    Nature. 1976 Jan 29;259(5541):333-5 PMID: 1250371
  26. The subunit structure of the eukaryotic chromosome.
    Nature. 1975 Jan 24;253(5489):245-9 PMID: 1167623
  27. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit.
    Cell. 1975 Apr;4(4):281-300 PMID: 1122558
  28. Super-helical model for nucleohistone.
    Nature. 1967 Jul 29;215(5100):508-9 PMID: 6057909
  29. Packing of DNA in the head of bacteriophage T2.
    J Mol Biol. 1967 Feb 14;23(3):523-33 PMID: 6032188
  30. Conformation studies on the sodium and cesium salts of calf thymus deoxyribonucleic acid (DNA).
    Biopolymers. 1966 Apr-May;4(4):429-40 PMID: 5948637
  31. An electron microscopic study of lambda and lambda-dg bacteriophage in thin sections.
    J Mol Biol. 1965 Dec;14(2):418-22 PMID: 5880858
  32. A model for particulate structure in chromatin.
    Nucleic Acids Res. 1974 Nov;1(11):1579-86 PMID: 10793713
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.75.1.103
Published
1978-01-00
Pages
103-7
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC411192
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.75.1.103 PMC Full Text View journal details
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