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PMID: 7393222 Published · ppublish English Journal Article

Conformational transitions in closed circular DNA molecules. II. Biological implications.

Molecular biology reports ·Vol. 6 ·No. 1 ·1980-03-31 ·Pages 11-5

Luchnik AN

Abstract

A model of regulation of gene action based on the theory of conformational transitions in closed circular DNA molecules is proposed and discussed in connection with the mechanisms of cellular differentiation. The model predicts two main types of regulation of gene action (1) the change in the topological linking number of the DNA loops leading to the change in the amount of the DNA segments present in the transcriptionally active A-form and (2) the change of some nucleotide sequences in closed superhelical DNA loops resulting in conformational transitions of some of the other sequences in the same loop. The first type of regulation may explain the mechanism of terminal differentiation of the stem cells and the changes accompanying the malignant transformation. The second one may explain the variegated position effect of the gene and determination of the stem cells during ontogenesis.

MeSH Terms
Chromatin/metabolism,ultrastructure DNA, Circular DNA, Superhelical Genes Mathematics Nucleic Acid Conformation Protein Biosynthesis Transcription, Genetic
Chemicals
Chromatin DNA, Circular DNA, Superhelical
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Luchnik A N
References (60)
60 references, click to expand
  1. Supercoiled DNA folded by non-histone proteins in cultured mammalian cells.
    Nature. 1975 Dec 4;258(5534):445-7 PMID: 1196378
  2. The human spermatozoa genome. Analysis by DNA reassociation kinetics.
    Biochim Biophys Acta. 1978 Dec 21;521(2):557-65 PMID: 737181
  3. Isolation of folded chromosomes from Mycoplasma hyorhinis.
    Nucleic Acids Res. 1977;4(5):1505-12 PMID: 896468
  4. DNA: models and reality.
    Nature. 1968 May 18;218(5142):633-7 PMID: 5651836
  5. Chromosomal protein interactions in chromatin and with DNA.
    J Mol Biol. 1976 Jun 14;104(1):25-58 PMID: 957433
  6. Histones bind more tightly to bromodeoxyuridine-substituted DNA than to normal DNA.
    Nucleic Acids Res. 1976 Sep;3(9):2183-91 PMID: 9622
  7. Effects of 5-bromo-2'-deoxyuridine and dimethyl sulfoxide on properties and structure of chromatin.
    J Mol Biol. 1974 Oct 15;89(1):137-62 PMID: 4475112
  8. Variation in DNA swivel enzyme activity during the mammalian cell cycle.
    Nucleic Acids Res. 1976 Dec;3(12):3305-11 PMID: 188020
  9. Genetic regulatory mechanisms in the synthesis of proteins.
    J Mol Biol. 1961 Jun;3:318-56 PMID: 13718526
  10. Altered histone-DNA interactions in rat liver chromatin containing 5-bromodeoxyuridine-substituted DNA.
    Cell Differ. 1977 Oct;6(3-4):241-51 PMID: 912759
  11. X-ray diffraction and molecular model building studies of the interaction of actinomycin with nucleic acids.
    Nature. 1963 May 11;198:538-40 PMID: 13952339
  12. Activity of DNA templates during cell division and cell differentiation.
    Nature. 1974 Mar 22;248(446):334-5 PMID: 4132100
  13. Transient inhibition of initiation of S-phase associated with dimethyl sulfoxide induction of murine erythroleukemia cells to erythroid differentiation.
    Proc Natl Acad Sci U S A. 1977 Jan;74(1):248-52 PMID: 64982
  14. The structure of a DNA-RNA hybrid.
    Proc Natl Acad Sci U S A. 1967 Jun;57(6):1804-10 PMID: 5340635
  15. Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance.
    Nature. 1968 Nov 9;220(5167):561-4 PMID: 5686726
  16. The effect of H1 histone on the action of DNA-relaxing enzyme.
    Nucleic Acids Res. 1977 Jan;4(1):117-27 PMID: 866171
  17. Optical rotatory dispersion and circular dichroism of rice dwarf virus ribonucleic acid.
    J Mol Biol. 1968 May 28;34(1):39-48 PMID: 5760455
  18. X-ray studies on two synthetic DNA copolymers.
    J Mol Biol. 1963 Apr;6:251-5 PMID: 14025400
  19. On the mechanism of SOS-repair and prophage induction: relaxation hypothesis.
    J Theor Biol. 1979 Mar 21;77(2):229-31 PMID: 480958
  20. Base composition changes in hepatocyte nuclei DNA of rats at different ages.
    Biochim Biophys Acta. 1978 Aug 23;520(1):38-51 PMID: 568004
  21. Lac operator analogues: bromodeoxyuridine substitution in the lac operator affects the rate of dissociation of the lac repressor.
    Proc Natl Acad Sci U S A. 1972 Sep;69(9):2574-6 PMID: 4560692
  22. Nonhistone proteins HMG1 and HMG2 change the DNA helical structure.
    Science. 1978 Mar 24;199(4335):1345-6 PMID: 628842
  23. The B to A transition of DNA in solution.
    J Mol Biol. 1974 Aug 25;87(4):817-33 PMID: 4427376
  24. Position-effect variegation.
    Adv Genet. 1968;14:133-69 PMID: 4884780
  25. Nucleosome structure II: structure of the SV40 minichromosome and electron microscopic evidence for reversible transitions of the nucleosome structure.
    Cold Spring Harb Symp Quant Biol. 1978;42 Pt 1:301-12 PMID: 209940
  26. Polymorphism of natural DNA.
    Nat New Biol. 1972 Oct 4;239(92):128-31 PMID: 4349669
  27. Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei.
    Proc Natl Acad Sci U S A. 1976 Nov;73(11):3966-70 PMID: 1069279
  28. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster.
    Cell. 1976 Nov;9(3):393-407 PMID: 825231
  29. Erythroleukemic differentiation.
    Annu Rev Biochem. 1978;47:419-48 PMID: 354501
  30. 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):640-4 PMID: 273227
  31. Histone changes during chromatin remodeling in embryogenesis.
    Cold Spring Harb Symp Quant Biol. 1978;42 Pt 1:421-31 PMID: 277356
  32. Conformational constraints in nuclear DNA.
    J Cell Sci. 1976 Nov;22(2):287-302 PMID: 1033937
  33. Amplification of moderately repetitive DNA sequences during chick cartilage differentiation.
    Proc Natl Acad Sci U S A. 1976 Oct;73(10):3428-32 PMID: 1068455
  34. The binding of lac repressor and the catabolite gene activator protein to halogen-substituted analogues of poly[d(A-T)].
    Biochim Biophys Acta. 1976 May 3;432(2):185-91 PMID: 773434
  35. Modulation of ribosomal RNA synthesis in Oncopeltus fasciatus: an electron microscopic study of the relationship between changes in chromatin structure and transcriptional activity.
    Cold Spring Harb Symp Quant Biol. 1978;42 Pt 2:723-40 PMID: 277315
  36. Superhelical DNA in yeast chromosomes.
    Exp Cell Res. 1977 Sep;108(2):473-8 PMID: 330181
  37. Morphology of transcriptionally active chromatin.
    Cold Spring Harb Symp Quant Biol. 1978;42 Pt 2:755-72 PMID: 277316
  38. Circular dichroism spectra of putative transcribed and repressed chromatin.
    Biochem Biophys Res Commun. 1973 May 1;52(1):202-7 PMID: 4736470
  39. Replication of circular DNA in eukaryotic cells.
    Annu Rev Biochem. 1974;43(0):695-719 PMID: 4605048
  40. Transcription of superhelical DNA from cell nuclei.
    Eur J Biochem. 1977 Jun 1;76(1):63-78 PMID: 328284
  41. Chromosomal subunits in active genes have an altered conformation.
    Science. 1976 Sep 3;193(4256):848-56 PMID: 948749
  42. Fine structure of active ribosomal genes.
    Chromosoma. 1976 Oct 12;58(1):33-9 PMID: 1001149
  43. Altered nucleosome structure containing DNA sequences complementary to 19S and 26S ribosomal RNA in Physarum polycephalum.
    Proc Natl Acad Sci U S A. 1978 Mar;75(3):1116-20 PMID: 274703
  44. Nuclear chromatin changes during erythroid differentiation of friend virus induced leukemic cells.
    Exp Cell Res. 1976 May;99(2):301-9 PMID: 57877
  45. The structure of histone-depleted metaphase chromosomes.
    Cell. 1977 Nov;12 (3):817-28 PMID: 922894
  46. The nucleosome repeat length increases during erythropoiesis in the chick.
    Nucleic Acids Res. 1978 Apr;5(4):1179-88 PMID: 565920
  47. Characterization of chromatin extensively substituted with 5-bromodeoxyuridine.
    Biochemistry. 1974 Oct 22;13(22):4609-16 PMID: 4279108
  48. Isolation of folded chromosomes from the yeast Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 1977 Jul;74(7):2850-4 PMID: 331318
  49. The dissociation of nuclear proteins from superhelical DNA.
    J Cell Sci. 1978 Feb;29:103-16 PMID: 627600
  50. Toward molecular mechanisms of developmental processes.
    Annu Rev Biochem. 1973;42:601-46 PMID: 4354314
  51. Theoretical calculations of base-base interactions in nucleic acids: II. Stacking interactions in polynucleotides.
    Nucleic Acids Res. 1978 May;5(5):1655-73 PMID: 662698
  52. Dependence of B-A conformational change in DNA on base composition.
    Nat New Biol. 1972 Mar 29;236(65):99-100 PMID: 4554380
  53. An electron microscopic comparison of transcription on linear and superhelical DNA.
    J Mol Biol. 1976 Jul 25;105(1):161-76 PMID: 792457
  54. Evidence for translocation of DNA sequences during sea urchin embryogenesis.
    Proc Natl Acad Sci U S A. 1978 Nov;75(11):5627-30 PMID: 364486
  55. Induction of murine erythroleukemia differentiation by actinomycin D.
    Proc Natl Acad Sci U S A. 1978 Jun;75(6):2795-9 PMID: 275849
  56. On the structure of the folded chromosome of Escherichia coli.
    J Mol Biol. 1972 Nov 14;71(2):127-47 PMID: 4564477
  57. Conformational transitions in closed circular DNA molecules. I. Topological and energetical considerations.
    Mol Biol Rep. 1980 Mar 31;6(1):3-9 PMID: 6248767
  58. A protein that preferentially binds Drosophila satellite DNA.
    Proc Natl Acad Sci U S A. 1979 Feb;76(2):726-30 PMID: 106393
  59. 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
  60. Variation of type-B DNA x-ray fiber diagrams with base composition.
    Proc Natl Acad Sci U S A. 1973 Jul;70(7):2167-70 PMID: 4352977
Article Info
Journal
Molecular biology reports
Abbr.
Mol Biol Rep
ISSN
0301-4851
Published
1980-03-31
Pages
11-5
Language
English
Region
Netherlands
NLM ID
0403234
Subset
IM
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