Home LiteratureArticle Details
PMID: 4011446 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo.

Nucleic acids research ·Vol. 13 ·No. 12 ·1985-06-25 ·Pages 4343-63

Haniford DB, Pulleyblank DE

Abstract

A 34 base pair tract of the simple repeating dinucleotide d(AT)n-d(AT)n cloned into a 2.4 kb polylinker plasmid vector undergoes a structural transition in response to negative superhelical coiling. The transition has been characterized by 2 dimensional gel electrophoresis, mapping of S1, P1 and T7 endonuclease 1 sensitive sites, and mapping of sites that are sensitive to modification by bromoacetaldehyde. After S1 nuclease treatment it is possible to trap supercoiled species that are nicked on one or both strands near the center of the palindrome. These data show that the alternate state adopted by the d(AT)n-dAT)n insert is a cruciform rather than a Z conformation. Unlike other B-cruciform transitions the transition in d(AT)n-d(AT)n has a low activation energy and the transition is facilitated by the presence of magnesium ions. Evidence from in-vivo topoisomer distributions is presented which shows that under conditions of blocked protein synthesis the d(AT)n-d(AT)n insert will spontaneously adopt the cruciform state in-vivo in E. coli.

MeSH Terms
Acetaldehyde/analogs & derivatives Base Composition Base Sequence Cloning, Molecular DNA, Superhelical/genetics Genetic Vectors Nucleic Acid Conformation Plasmids Poly dA-dT/genetics Polydeoxyribonucleotides/genetics
Chemicals
DNA, Superhelical Polydeoxyribonucleotides bromoacetaldehyde Poly dA-dT Acetaldehyde
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Haniford D B
Pulleyblank D E
References (43)
43 references, click to expand
  1. Quantum mechanical study of bases interactions in various associates in atomic dipole approximation.
    J Theor Biol. 1976 Jul 7;59(2):303-18 PMID: 957693
  2. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster.
    Cell. 1976 Nov;9(3):393-407 PMID: 825231
  3. DNA gyrase: an enzyme that introduces superhelical turns into DNA.
    Proc Natl Acad Sci U S A. 1976 Nov;73(11):3872-6 PMID: 186775
  4. The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity.
    Nucleic Acids Res. 1977;4(5):1183-205 PMID: 197488
  5. Energy coupling in DNA gyrase and the mechanism of action of novobiocin.
    Proc Natl Acad Sci U S A. 1978 Oct;75(10):4838-42 PMID: 368801
  6. Helical repeat of DNA in solution.
    Proc Natl Acad Sci U S A. 1979 Jan;76(1):200-3 PMID: 284332
  7. Review: ethidium fluorescence assays. Part 1. Physicochemical studies.
    Nucleic Acids Res. 1979 Oct 10;7(3):547-69 PMID: 41222
  8. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein.
    J Mol Biol. 1979 Jul 15;131(4):669-80 PMID: 513130
  9. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells.
    Cell. 1980 Oct;21(3):773-83 PMID: 6254668
  10. Polymorphism of DNA double helices.
    J Mol Biol. 1980 Oct 15;143(1):49-72 PMID: 7441761
  11. DNA supercoiling: another level for regulating gene expression.
    Cell. 1981 Jun;24(3):599-600 PMID: 6265097
  12. Helical periodicity of DNA, Poly(dA) . poly(dT) and poly(dA-dT). poly(dA-dT) in solution.
    Eur J Biochem. 1981 Aug;118(2):215-22 PMID: 7285918
  13. Energetic and structural inter-relationship between DNA supercoiling and the right- to left-handed Z helix transitions in recombinant plasmids.
    J Biol Chem. 1982 Sep 10;257(17):10159-65 PMID: 6286642
  14. T4 endonuclease VII cleaves holliday structures.
    Cell. 1982 Jun;29(2):357-65 PMID: 6288255
  15. Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling.
    Proc Natl Acad Sci U S A. 1982 Aug;79(15):4560-4 PMID: 6956879
  16. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding.
    Cell. 1982 Dec;31(2 Pt 1):309-18 PMID: 7159926
  17. Transcription of DNA injected into Xenopus oocytes is influenced by template topology.
    Nature. 1983 Mar 3;302(5903):38-43 PMID: 6828158
  18. 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
  19. A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin.
    Cell. 1983 Apr;32(4):1191-203 PMID: 6301683
  20. Conformational flexibility of junctions between contiguous B- and Z-DNAs in supercoiled plasmids.
    Proc Natl Acad Sci U S A. 1983 May;80(9):2447-51 PMID: 6302683
  21. DNA supercoiling: changes during cellular differentiation and activation of chromatin transcription.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 2:793-801 PMID: 6305587
  22. Sites required for position-effect regulation of mating-type information in yeast.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 2:989-98 PMID: 6345082
  23. Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions.
    Cell. 1983 Jul;33(3):817-29 PMID: 6871994
  24. Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling.
    Cell. 1983 Aug;34(1):105-13 PMID: 6309403
  25. Slow cruciform transitions in palindromic DNA.
    Proc Natl Acad Sci U S A. 1983 Sep;80(18):5545-9 PMID: 6577442
  26. Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis.
    FEBS Lett. 1983 Mar 21;153(2):298-302 PMID: 6352326
  27. Energetics of B-to-Z transition in DNA.
    Proc Natl Acad Sci U S A. 1983 Oct;80(20):6206-10 PMID: 6578505
  28. Dynamics of cruciform extrusion in supercoiled DNA: use of a synthetic inverted repeat to study conformational populations.
    EMBO J. 1983;2(4):527-33 PMID: 6628359
  29. A method for the purification of E. coli plasmid DNA by homogeneous lysis and polyethylene glycol precipitation.
    Mol Biol Rep. 1983 Aug;9(3):191-5 PMID: 6355817
  30. Formation of Z-DNA in negatively supercoiled plasmids is sensitive to small changes in salt concentration within the physiological range.
    EMBO J. 1983;2(5):649-55 PMID: 6315414
  31. Cruciform-resolvase interactions in supercoiled DNA.
    Cell. 1984 Feb;36(2):413-22 PMID: 6319022
  32. Thermodynamics of the B-Z transition in superhelical DNA.
    Nature. 1984 Feb 2-8;307(5950):481-2 PMID: 6694740
  33. Left-handed Z-DNA regions are present in negatively supercoiled bacteriophage PM2 DNA.
    EMBO J. 1983;2(12):2123-8 PMID: 6365531
  34. Chromatin assembly in Xenopus oocytes: in vivo studies.
    Cell. 1984 May;37(1):21-32 PMID: 6202419
  35. Intervening sequences in human fetal globin genes adopt left-handed Z helices.
    J Biol Chem. 1984 Jun 10;259(11):7268-74 PMID: 6202693
  36. Regulation of bacterial DNA supercoiling: plasmid linking numbers vary with growth temperature.
    Proc Natl Acad Sci U S A. 1984 Jul;81(13):4046-50 PMID: 6377307
  37. The genetic control of DNA supercoiling in Salmonella typhimurium.
    EMBO J. 1984 Aug;3(8):1745-52 PMID: 6090123
  38. Possible structures of homopurine-homopyrimidine S1-hypersensitive sites.
    Nucleic Acids Res. 1984 Nov 12;12(21):8059-72 PMID: 6095187
  39. Torsional stress promotes the DNAase I sensitivity of active genes.
    Cell. 1984 Dec;39(3 Pt 2):469-78 PMID: 6096006
  40. Thermodynamics of the ColE1 cruciform. Comparisons between probing and topological experiments using single topoisomers.
    J Mol Biol. 1984 Nov 25;180(1):179-200 PMID: 6096558
  41. Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence.
    Cell. 1985 Jan;40(1):129-37 PMID: 2981624
  42. The in-vivo occurrence of Z DNA.
    J Biomol Struct Dyn. 1983 Dec;1(3):593-609 PMID: 6401120
  43. X-ray studies on two synthetic DNA copolymers.
    J Mol Biol. 1963 Apr;6:251-5 PMID: 14025400
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/13.12.4343
Published
1985-06-25
Pages
4343-63
Language
English
Region
England
NLM ID
0411011
PMCID
PMC321792
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/13.12.4343 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: [email protected]

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