• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Mar 11, 1985; 13(5): 1683–1701.
PMCID: PMC341105

Concordance of experimentally mapped or predicted Z-DNA sites with positions of selected alternating purine-pyrimidine tracts.


The recent electronmicroscopic and biochemical mapping of Z-DNA sites in phi X174, SV40, pBR322 and PM2 DNAs has been used to determine two sets of criteria for identification of potential Z-DNA sequences in natural DNA genomes. The prediction of potential Z-DNA tracts and corresponding statistical analysis of their occurrence have been made on a sample of 14 DNA genomes. Alternating purine and pyrimidine tracts longer than 5 base pairs in length and their clusters (quasi alternating fragments) in the 14 genomes studied are under-represented compared to the expectation from corresponding random sequences. The fragments [d(G X C)]n and [d(C X G)]n (n greater than or equal to 3) in general do not occur in circular DNA genomes and are under-represented in the linear DNAs of phages lambda and T7, whereas in linear genomes of adenoviruses they are strongly over-represented. With minor exceptions, potential Z-DNA sites are also under-represented compared to random sequences. In the 14 genomes studied, predicted Z-DNA tracts occur in non-coding as well as in protein coding regions. The predicted Z-DNA sites in phi X174, SV40, pBR322 and PM2 correspond well with those mapped experimentally. A complete listing together with a compact graphical representation of alternating purine-pyrimidine fragments and their Z-forming potential are presented.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.3M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Pohl FM, Jovin TM. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol. 1972 Jun 28;67(3):375–396. [PubMed]
  • Wang AJ, Quigley GJ, Kolpak FJ, van der Marel G, van Boom JH, Rich A. Left-handed double helical DNA: variations in the backbone conformation. Science. 1981 Jan 9;211(4478):171–176. [PubMed]
  • Drew HR, Dickerson RE. Structure of a B-DNA dodecamer. III. Geometry of hydration. J Mol Biol. 1981 Sep 25;151(3):535–556. [PubMed]
  • Jovin TM, McIntosh LP, Arndt-Jovin DJ, Zarling DA, Robert-Nicoud M, van de Sande JH, Jorgenson KF, Eckstein F. Left-handed DNA: from synthetic polymers to chromosomes. J Biomol Struct Dyn. 1983 Oct;1(1):21–57. [PubMed]
  • Nordheim A, Lafer EM, Peck LJ, Wang JC, Stollar BD, Rich A. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell. 1982 Dec;31(2 Pt 1):309–318. [PubMed]
  • Singleton CK, Klysik J, Stirdivant SM, Wells RD. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 1982 Sep 23;299(5881):312–316. [PubMed]
  • Pohl FM, Thomae R, DiCapua E. Antibodies to Z-DNA interact with form V DNA. Nature. 1982 Dec 9;300(5892):545–546. [PubMed]
  • Di Capua E, Stasiak A, Koller T, Brahms S, Thomae R, Pohl FM. Torsional stress induces left-handed helical stretches in DNA of natural base sequence: circular dichroism and antibody binding. EMBO J. 1983;2(9):1531–1535. [PMC free article] [PubMed]
  • Wang JC, Peck LJ, Becherer K. DNA supercoiling and its effects on DNA structure and function. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):85–91. [PubMed]
  • Peck LJ, Wang JC. Energetics of B-to-Z transition in DNA. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6206–6210. [PMC free article] [PubMed]
  • Zarling DA, Arndt-Jovin DJ, McIntosh LP, Robert-Nicoud M, Jovin TM. Interactions of anti-poly[d(G-br5C)] IgG with synthetic, viral and cellular Z DNAs. J Biomol Struct Dyn. 1984 Mar;1(5):1081–1107. [PubMed]
  • Zarling DA, Arndt-Jovin DJ, Robert-Nicoud M, McIntosh LP, Thomae R, Jovin TM. Immunoglobulin recognition of synthetic and natural left-handed Z DNA conformations and sequences. J Mol Biol. 1984 Jul 5;176(3):369–415. [PubMed]
  • Nordheim A, Pardue ML, Lafer EM, Möller A, Stollar BD, Rich A. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature. 1981 Dec 3;294(5840):417–422. [PubMed]
  • Lemeunier F, Derbin C, Malfoy B, Leng M, Taillandier E. Identification of left-handed Z-DNA by indirect immunofluorescence in polytene chromosomes of Chironomus thummi thummi. Exp Cell Res. 1982 Oct;141(2):508–513. [PubMed]
  • Arndt-Jovin DJ, Robert-Nicoud M, Zarling DA, Greider C, Weimer E, Jovin TM. Left-handed Z-DNA in bands of acid-fixed polytene chromosomes. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4344–4348. [PMC free article] [PubMed]
  • Robert-Nicoud M, Arndt-Jovin DJ, Zarling DA, Jovin TM. Immunological detection of left-handed Z DNA in isolated polytene chromosomes. Effects of ionic strength, pH, temperature and topological stress. EMBO J. 1984 Apr;3(4):721–731. [PMC free article] [PubMed]
  • Russell WC, Precious B, Martin SR, Bayley PM. Differential promotion and suppression of Z leads to B transitions in poly[d(G-C)] by histone subclasses, polyamino acids and polyamines. EMBO J. 1983;2(10):1647–1653. [PMC free article] [PubMed]
  • Nordheim A, Rich A. Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences. Nature. 1983 Jun 23;303(5919):674–679. [PubMed]
  • Azorin F, Nordheim A, Rich A. 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):649–655. [PMC free article] [PubMed]
  • Rich A, Nordheim A, Azorin F. Stabilization and detection of natural left-handed Z-DNA. J Biomol Struct Dyn. 1983 Oct;1(1):1–19. [PubMed]
  • Rich A. Right-handed and left-handed DNA: conformational information in genetic material. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):1–12. [PubMed]
  • Stockton JF, Miller FD, Jorgenson KF, Zarling DA, Morgan AR, Rattner JB, van de Sande JH. Left-handed Z-DNA regions are present in negatively supercoiled bacteriophage PM2 DNA. EMBO J. 1983;2(12):2123–2128. [PMC free article] [PubMed]
  • Miller FD, Jorgenson KF, Winkfein RJ, van de Sande JH, Zarling DA, Stockton J, Rattner JB. Natural occurrence of left-handed (Z) regions in PM2 DNA. J Biomol Struct Dyn. 1983 Dec;1(3):611–620. [PubMed]

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


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem Compound links
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...