Stabilization of Z DNA in vivo by localized supercoiling.

Biological processes such as transcription may generate domains of supercoiling on a circular DNA. The existence of these domains in Escherichia coli was investigated by the ability of different lengths of (CG) tracts, cloned upstream or downstream from the tetracycline resistance gene (tet) of pBR322, to adopt the Z structure in vivo. Segments as short as 12 base pairs adopt the Z form when cloned upstream from the tet gene (Eco RI site), whereas no Z DNA was detected when this sequence was cloned downstream (Sty I site), even with a 74-base pair (CG) tract that requires less supercoiling than shorter tracts for the B-Z transition. Hence the localized supercoil density in pBR322 can be as high as -0.038 and as low as -0.021 at different loci. These data demonstrate the existence of the Z structure for commonly found natural sequences and support the notion of domains of negative supercoiling in vivo.

[1]  E. Paleček,et al.  Probing of DNA polymorphic structure in the cell with osmium tetroxide. , 1988, Biochemical and biophysical research communications.

[2]  R. Sternglanz,et al.  Transcription-dependent DNA supercoiling in yeast DNA topoisomerase mutants , 1988, Cell.

[3]  J. Gralla,et al.  DNA supercoiling promotes formation of a bent repression loop in lac DNA. , 1987, Journal of molecular biology.

[4]  J. Lodge,et al.  Formation of supercoiling domains in plasmid pBR322 , 1989, Journal of bacteriology.

[5]  R. Wells,et al.  Left-handed Z-DNA and genetic recombination. , 1989, Progress in nucleic acid research and molecular biology.

[6]  J. Clark,et al.  Functional effects of cis-thymine glycol lesions on DNA synthesis in vitro. , 1987, Biochemistry.

[7]  J. Wang,et al.  Involvement of DNA topoisomerase I in transcription of human ribosomal RNA genes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Rich,et al.  Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution , 1985, Cell.

[9]  R. Wells,et al.  The facile generation of covalently closed, circular DNAs with defined negative superhelical densities. , 1982, Analytical biochemistry.

[10]  E. Sage,et al.  Conformation of poly(dG-dC) . poly(dG-dC) modified by the carcinogens N-acetoxy-N-acetyl-2-aminofluorene and N-hydroxy-N-2-aminofluorene. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Wells,et al.  Tetracycline promoter mutations decrease non-B DNA structural transitions, negative linking differences and deletions in recombinant plasmids in Escherichia coli. , 1989, Journal of molecular biology.

[12]  R. Wells,et al.  The B- to Z-DNA equilibrium in vivo is perturbed by biological processes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[13]  W. Jelinek,et al.  Repetitive sequences in eukaryotic DNA and their expression. , 1982, Annual review of biochemistry.

[14]  A. Rich,et al.  Induction of the Z conformation in poly(dG-dC).poly(dG-dC) by binding of N-2-acetylaminofluorene to guanine residues. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[15]  L. Bossi,et al.  Transcription induces gyration of the DNA template in Escherichia coli. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[16]  W. Herr.  Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[17]  N. Cozzarelli,et al.  Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. , 1987, Journal of molecular biology.

[18]  N. Rousseau,et al.  A study of the B-Z transition of the AC-rich region of the repeat unit of a satellite DNA from Cebus by means of chemical probes. , 1988, Journal of Biological Chemistry.

[19]  J. Wang,et al.  Supercoiling of the DNA template during transcription. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Characteristics of Z-DNA helices formed by imperfect (purine-pyrimidine) sequences in plasmids. , 1988, The Journal of biological chemistry.

[21]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[22]  Leroy F. Liu,et al.  Transcription generates positively and negatively supercoiled domains in the template , 1988, Cell.

[23]  D. Lilley,et al.  Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene. , 1985, Journal of molecular biology.

[24]  R. Bauerle,et al.  The functional organization of the tryptophan gene cluster in Salmonella typhimurium. , 1966, Proceedings of the National Academy of Sciences of the United States of America.

[25]  G. Giaever,et al.  Supercoiling of intracellular DNA can occur in eukaryotic cells , 1988, Cell.

[26]  R. Wells,et al.  The role of sequence in the stabilization of left-handed DNA helices in vitro and in vivo. , 1988, Biochimica et biophysica acta.

[27]  J. Gralla,et al.  High-resolution analysis of lac transcription complexes inside cells. , 1986, Biochemistry.

[28]  E. Trifonov,et al.  Unusual frequencies of certain alternating purine‐pyrimidine runs in natural DNA sequences: relation to Z‐DNA , 1985, FEBS letters.

[29]  C. Alonso,et al.  Z-DNA in transcriptionally active chromosomes. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[30]  K. Drlica,et al.  DNA supercoiling and prokaryotic transcription , 1989, Cell.

[31]  R. Wells,et al.  Intramolecular DNA triplexes in supercoiled plasmids. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Alfred Nordheim,et al.  THE CHEMISTRY AND BIOLOGY OF LEFT-HANDED Z-DNA , 1984 .

[33]  A. Rich,et al.  The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain , 1989, The Journal of cell biology.

[34]  D. Lilley,et al.  Localized chemical hyperreactivity in supercoiled DNA: evidence for base unpairing in sequences that induce low-salt cruciform extrusion. , 1989, Biochemistry.

[35]  C. Higgins,et al.  DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression , 1988, Journal of bacteriology.

[36]  R. Wells,et al.  Reaction conditions affect the specificity of bromoacetaldehyde as a probe for DNA cruciforms and B-Z junctions. , 1987, Nucleic acids research.

[37]  Y. Kohwi,et al.  Unusual conformational effect exerted by Z-DNA upon its neighboring sequences. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J. Gralla,et al.  KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. , 1989, The Journal of biological chemistry.

[39]  R. Wells,et al.  Left-handed Z-DNA binding by the recA protein of Escherichia coli. , 1987, The Journal of biological chemistry.

[40]  R. Sternglanz,et al.  Need for DNA topoisomerase activity as a swivel for DNA replication for transcription of ribosomal RNA , 1987, Nature.

[41]  R. Wells,et al.  Left-handed DNA in vivo. , 1987, Science.

[42]  E. Paleček,et al.  Site-specific OsO4 modification of the B-Z junctions formed at the (dA-dC)32 region in supercoiled DNA. , 1986, The Journal of biological chemistry.

[43]  H. Hamada,et al.  Potential Z-DNA forming sequences are highly dispersed in the human genome , 1982, Nature.

[44]  S. Wallace,et al.  Thymine glycols and urea residues in M13 DNA constitute replicative blocks in vitro. , 1985, Nucleic acids research.