Home LiteratureArticle Details
PMID: 9600903 Published · ppublish English Journal Article

Submillimolar levels of calcium regulates DNA structure at the dinucleotide repeat (TG/AC)n.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 95 ·No. 11 ·1998-05-26 ·Pages 5981-6

Dobi A, v Agoston D

Abstract

Submillimolar levels of calcium, similar to the physiological total (bound + free) intranuclear concentration (0.01-1 mM), induced a conformational change within d(TG/AC)n, one of the frequent dinucleotide repeats of the mammalian genome. This change is calcium-specific, because no other tested cation induced it and it was detected as a concentration-dependent transition from B- to a non-B-DNA conformation expanding from 3' end toward the 5' of the repeat. Genomic footprinting of various rat brain regions revealed the existence of similar non-B-DNA conformation within a d(TG/AC)28 repeat of the endogenous enkephalin gene only in enkephalin-expressing caudate nucleus and not in the nonexpressing thalamus. Binding assays demonstrated that DNA could bind calcium and can compete with calmodulin for calcium.

MeSH Terms
Animals Base Sequence Brain/metabolism Calcium/metabolism,pharmacology DNA/chemistry,drug effects,physiology Molecular Sequence Data Nucleic Acid Conformation/drug effects Nucleotides/chemistry,physiology Rats
Chemicals
Nucleotides DNA Calcium
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Dobi A
Molecular Control of Neurodifferentiation, Laboratory of Developmental Neurobiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
v Agoston D
References (47)
47 references, click to expand
  1. A new method for sequencing DNA.
    Proc Natl Acad Sci U S A. 1977 Feb;74(2):560-4 PMID: 265521
  2. Identification of processes that influence negative supercoiling in the human c-myc gene.
    Biochim Biophys Acta. 1997 May 30;1352(2):213-21 PMID: 9199252
  3. Calmodulin.
    Annu Rev Biochem. 1980;49:489-515 PMID: 6250447
  4. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC).
    Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619-23 PMID: 6262820
  5. Potential Z-DNA forming sequences are highly dispersed in the human genome.
    Nature. 1982 Jul 22;298(5872):396-8 PMID: 6283389
  6. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions.
    Nature. 1983 Apr 14;302(5909):632-4 PMID: 6835398
  7. The chemistry and biology of left-handed Z-DNA.
    Annu Rev Biochem. 1984;53:791-846 PMID: 6383204
  8. Selective binding of the estradiol receptor to a region at least one kilobase upstream from the rat prolactin gene.
    DNA. 1985 Feb;4(1):1-9 PMID: 3971854
  9. Enhanced gene expression by the poly(dT-dG).poly(dC-dA) sequence.
    Mol Cell Biol. 1984 Dec;4(12):2622-30 PMID: 6098815
  10. Protein kinases in the brain.
    Annu Rev Biochem. 1985;54:931-76 PMID: 2411213
  11. Subcellular concentrations of calcium, zinc, and magnesium in benign nodular hyperplasia of the human prostate: X-ray microanalysis of freeze-dried cryosections.
    Cancer Res. 1987 Jan 1;47(1):323-8 PMID: 2431766
  12. Electron probe microanalysis of the subcellular compartments of bovine adrenal chromaffin cells. Comparison of chromaffin granules in situ and in vitro.
    J Biol Chem. 1988 Jan 25;263(3):1488-93 PMID: 3335554
  13. Quantitative imaging of boron, calcium, magnesium, potassium, and sodium distributions in cultured cells with ion microscopy.
    Anal Chem. 1989 Dec 15;61(24):2690-5 PMID: 2619055
  14. Z-DNA-binding proteins. Identification critically depends on the proper choice of ligands.
    J Biol Chem. 1990 Nov 5;265(31):19112-5 PMID: 2172244
  15. Calcium channels, stores, and oscillations.
    Annu Rev Cell Biol. 1990;6:715-60 PMID: 2177344
  16. Transcription is associated with Z-DNA formation in metabolically active permeabilized mammalian cell nuclei.
    Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2259-63 PMID: 2006166
  17. Local supercoil-stabilized DNA structures.
    Crit Rev Biochem Mol Biol. 1991;26(2):151-226 PMID: 1914495
  18. Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genomes.
    J Biomol Struct Dyn. 1991 Oct;9(2):387-97 PMID: 1741969
  19. Calcium-induced release of calcium regulates differentiation of cultured spinal neurons.
    Neuron. 1991 Nov;7(5):787-96 PMID: 1742025
  20. Osmium tetroxide reactivity of DNA bases in nucleotide sequencing and probing of DNA structure.
    Gen Physiol Biophys. 1991 Oct;10(5):461-73 PMID: 1816027
  21. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes.
    J Biol Chem. 1992 Jun 15;267(17):11846-55 PMID: 1601856
  22. Primary sequence of -1436 to +53 bp of the rat preproenkephalin gene putative Z-DNA and regulatory motifs.
    Biochim Biophys Acta. 1992 Jul 15;1131(3):349-51 PMID: 1627654
  23. Intranuclear Ca2+ transients during neurite regeneration of an adult mammalian neuron.
    Proc Natl Acad Sci U S A. 1992 Sep 1;89(17):7978-82 PMID: 1518824
  24. Zuotin, a putative Z-DNA binding protein in Saccharomyces cerevisiae.
    EMBO J. 1992 Oct;11(10):3787-96 PMID: 1396572
  25. Ca2+ binding environments on natural and synthetic polymeric DNA's.
    J Biomol Struct Dyn. 1992 Oct;10(2):333-43 PMID: 1466813
  26. m-Calpain requires DNA for activity on nuclear proteins at low calcium concentrations.
    J Biol Chem. 1993 Jan 5;268(1):653-7 PMID: 8416968
  27. B-DNA to Z-DNA structural transitions in the SV40 enhancer: stabilization of Z-DNA in negatively supercoiled DNA minicircles.
    Biochemistry. 1993 Mar 9;32(9):2167-76 PMID: 8382945
  28. Z-DNA binding protein from chicken blood nuclei.
    Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3339-42 PMID: 8475077
  29. Nucleotide repeats. Slippery DNA and diseases.
    Nature. 1993 Sep 16;365(6443):207-8 PMID: 8371775
  30. The loop sequence plays crucial roles for isomerization of intramolecular DNA triplexes in supercoiled plasmids.
    J Mol Biol. 1994 Jan 7;235(1):185-97 PMID: 8289240
  31. The non-B-DNA structure of d(CA/TG)n differs from that of Z-DNA.
    Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1898-902 PMID: 8127902
  32. Association of poly(CA).poly(TG) DNA fragments into four-stranded complexes bound by HMG1 and 2.
    Science. 1994 Apr 15;264(5157):433-6 PMID: 8153633
  33. Imaging of total intracellular calcium and calcium influx and efflux in individual resting and stimulated tumor mast cells using ion microscopy.
    J Biol Chem. 1994 May 27;269(21):15186-94 PMID: 8195154
  34. Calcium regulation of gene expression in neuronal cells.
    J Neurobiol. 1994 Mar;25(3):294-303 PMID: 7910846
  35. New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility.
    Prog Nucleic Acid Res Mol Biol. 1994;47:195-270 PMID: 8016321
  36. The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA.
    Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9549-53 PMID: 7937803
  37. Guanine specific chemical sequencing of DNA by osmium tetroxide.
    Nucleic Acids Res. 1994 Nov 11;22(22):4846-7 PMID: 7984442
  38. Regulation of nuclear calcium concentration.
    Ciba Found Symp. 1995;188:252-62; discussion 262-6 PMID: 7587621
  39. Protein-DNA interactions during phenotypic differentiation.
    Mol Neurobiol. 1995 Apr-Jun;10(2-3):185-203 PMID: 7576307
  40. Calcium waves, gradients and oscillations. Proceedings of a symposium. London, 26-28 April 1994.
    Ciba Found Symp. 1995;188:1-291 PMID: 7587612
  41. The elemental principles of calcium signaling.
    Cell. 1995 Dec 1;83(5):675-8 PMID: 8521483
  42. The biology of left-handed Z-DNA.
    J Biol Chem. 1996 May 17;271(20):11595-8 PMID: 8662853
  43. Intercalation, DNA kinking, and the control of transcription.
    Science. 1996 Feb 9;271(5250):778-84 PMID: 8628992
  44. Hyper-negative template DNA supercoiling during transcription of the tetracycline-resistance gene in topA mutants is largely constrained in vivo.
    Nucleic Acids Res. 1996 Aug 1;24(15):3093-9 PMID: 8760899
  45. A nuclear traffic jam: unraveling multicomponent machines and compartments.
    Curr Opin Cell Biol. 1996 Jun;8(3):299-302 PMID: 8743878
  46. Detection of conformation bias between the complementary strands of deoxynucleotide repeat (TG/AC)n.
    Electrophoresis. 1997 Jan;18(1):12-6 PMID: 9059814
  47. New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis, and properties of prototype structures.
    Biochemistry. 1980 May 27;19(11):2396-404 PMID: 6770893
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.95.11.5981
Published
1998-05-26
Pages
5981-6
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC27571
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.95.11.5981 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2