Characterization of Genomic Poly(dT-dG) · Poly(dC-dA) Sequences: Structure, Organization, and Conformation

LITERATURE CITED

• Aiken, J. M., McKenzee, D., Zhao, H.-Z., State, J. C., and Dixon, G. H. 1983. Sequence homologies in the protamine gene family of rainbow trout. Nucleic Acids Res. 11:4907–4922.
   PubMedGoogle Scholar
• Arndt-Jovin, D. J., Robert-Nicoud, M., Zarling, D. A., Grider, C., Weimer, E., and Jovin, T. M. 1983. Left-handed DNA in bands of acid-fixed polytene chromosomes. Proc. Natl. Acad. Sci. U.S.A. 80:4344–4348.
   PubMed Web of Science ®Google Scholar
• Azorin, F., Nordheim, A., and Rich, A. 1983. Formation of Z-DNA in negatively supercoiled plasmids is sensitive to small changes in salt concentration within physiological range. EMBO J. 2:649–655.
   PubMed Web of Science ®Google Scholar
• Bauer, W. R. 1978. Structure and reactions of closed duplex DNA. Annu. Rev. Biophys. Bioeng. 7:287–313.
   PubMedGoogle Scholar
• Campbell, D. A., van Bree, M. P., and Boothroyd, J. C. 1984. The 5′-limit of transposition and upstream barren region of a try-panosome VSG gene: tandem 76 base-pair repeats flanking (TAAW Nucleic Acids Res. 11:8087–8101.
   Google Scholar
• Deininger, P. L., Jolly, D. J., Rubin, C. M., Friedman, T., and Schmid, C. W. 1981. Base sequence studies of 300 nucleotide renatured repetitive human DNA clones. J. Mol. Biol. 151:17–33.
   PubMed Web of Science ®Google Scholar
• Dolan, M., Dogson, J. B., and Engel, J. D. 1983. Analysis of the adult chicken β-globin gene. Nucleotide sequence of the locus, microheterogeneity at the 5-end of β-globin mRNA, and aberrant nuclear RNA species. J. Biol. Chem. 258:3983–3990.
   PubMedGoogle Scholar
• Hamada, H., and Kakunaga, T. 1982. Potential Z-DNA sequences are highly dispersed in the human genome. Nature (London) 298:396–398.
   PubMed Web of Science ®Google Scholar
• Hamada, H., Petrino, M. G., and Kakunaga, T. 1982. A novel repeated element with Z-DNA forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc. Natl. Acad. Sci. U.S.A. 79:6465–6469.
   PubMed Web of Science ®Google Scholar
• Hamada, H., Petrino, M. G., and Kakunaga, T. 1982. Molecular structure and evolutionary origin of human cardiac muscle actin gene. Proc. Natl. Acad. Sci. U.S.A. 79:5901–5905.
   PubMed Web of Science ®Google Scholar
• Hamada, H., Seidman, M., Howard, B. H., and Gorman, C. M. 1984. Enhanced gene expression by the poly(dT-dG) · poly(dC-dA) sequence. Mol. Cell. Biol. 4:2622–2630.
   PubMed Web of Science ®Google Scholar
• Haniford, D. B., and Pulleyblank, D. E. 1983. Facile transition of poly[d(TG) · (CA)] into a left-handed helix in physiological conditions. Nature (London) 302:632–634.
   PubMed Web of Science ®Google Scholar
• Klysik, J., Stirdivant, S. M., Singleton, C. K., Zacharias, W., and Wells, R. D. 1983. Effects of 5 cytosine methylation on the B-Z transition in DNA restriction fragments and recombinant plasmids. J. Mol. Biol. 168:51–71.
   PubMed Web of Science ®Google Scholar
• Lafer, E. M., Moller, A., Nordheim, A., Stollar, B. D., and Rich, A. 1981. Antibodies specific for left-handed Z-DNA. Proc. Natl. Acad. Sci. U.S.A. 78:3546–3550.
   PubMed Web of Science ®Google Scholar
• Larson, A., and Weintraub, H. 1982. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chicken globin chromatin. Cell 29:609–622.
   PubMed Web of Science ®Google Scholar
• Lilley, D. M. J. 1980. The inverted repeats as a recognizable structural feature in supercoiled DNA molecule. Proc. Natl. Acad. Sci. U.S.A. 77:6468–6472.
   PubMed Web of Science ®Google Scholar
• Maxam, A., and Gilbert, W. 1980. Sequencing of end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65:499–560.
   PubMedGoogle Scholar
• Miesfield, R., Krystal, M., and Arnheim, N. 1981. A member of new repeated sequence family which is conserved throughout evolution is found between the human δ and β globin genes. Nucleic Acids Res. 9:5931–5947.
   PubMedGoogle Scholar
• Nishioka, Y., and Leder, P. 1980. Organization and complete nucleotide sequence of identical embryonic and plasmocytoma κ V-region genes. j. Biol. Chem. 255:3691–3694.
   Google Scholar
• Nordheim, A., Pardue, M. L., Lafer, E. M., Moller, A., Stollar, B. D., and Rich, A. 1981. Antibodies to left-handed Z-DNA bind to interbands regions of Drosophila polytene chromosomes. Nature (London) 294:417–422.
   PubMed Web of Science ®Google Scholar
• Nordheim, A., and Rich, A. 1983. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell 31:309–318.
   Google Scholar
• Nordheim, A., and Rich, A. 1983. The sequence (dC-dA)n · (dT-dG)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc. Natl. Acad. Sci. U.S.A. 80:1821–1825.
   PubMed Web of Science ®Google Scholar
• Nordheim, A., and Rich, A. 1983. Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences. Nature (London) 303:674–679.
   PubMed Web of Science ®Google Scholar
• Peck, L. J., Nordheim, A., Rich, A., and Wang, J. C. 1982. 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. 79:4560–4564.
   PubMed Web of Science ®Google Scholar
• Peck, L. J., and Wang, J. C. 1983. Energetics of B-to-Z transition in DNA. Proc. Natl. Acad. Sci. U.S.A. 80:6206–6210.
   PubMed Web of Science ®Google Scholar
• Rogers, J. 1983. CACA sequences-the ends and the means. Nature (London) 305:101–102.
   PubMedGoogle Scholar
• Saffer, J. D., and Lerman, M. I. 1983. An unusual class of Alu sequences containing a potential Z-DNA segment. Mol. Cell. Biol. 2:960–964.
   Google Scholar
• Sawada, I., Beal, M. P., Shen, C. K.-J., Chapman, B., Wilson, A. C., and Schmid, C. W. 1983. Intergenic DNA sequences flanking the pseudo alpha globin genes of human and chimpanzee. Nucleic Acids Res. 11:8087–8101.
   PubMedGoogle Scholar
• Sinden, R. R., Carlson, J. O., and Pettyohn, D. E. 1980. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurement in insect and human cells. Cell 21:773–783.
   PubMed Web of Science ®Google Scholar
• Singleton, C. K., Kilpatrick, M. W., and Wells, R. D. 1984. Sj nuclease recognizes DNA conformational junctions between left-handed helical (dT-dG)n · (dC-dA)n and contiguous right-handed sequences. J. Biol. Chem. 259:1963–1967.
   PubMed Web of Science ®Google Scholar
• Singleton, C. K., Klysik, J., Stidivant, S. M., and Wells, R. D. 1982. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature (London) 299:475–485.
   PubMedGoogle Scholar
• Singleton, C. K., and Wells, R. D. 1982. The facile generation of covalently closed, circular DNAs with defined negative super-helical densities. Anal. Biochem. 122:253–257.
   PubMed Web of Science ®Google Scholar
• Slightom, J. L., Blechl, A. E., and Smithies, O. 1980. Human fetal Gγ- and Aγ-globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes. Cell 21:627–638.
   PubMed Web of Science ®Google Scholar
• Stanton, L. W., Watt, R., and Marcu, K. B. 1983. Translocation, breakage and truncated transcripts of c-myc oncogene in murine plasmocytomas. Nature (London) 303:401–406.
   PubMed Web of Science ®Google Scholar
• Stirdivant, S. M., Klysik, J., and Wells, R. D. 1982. Energetics and structural inter-relationship between DNA supercoiling and the right- to left-handed Z helix transition in recombinant plasmids. J. Biol. Chem. 257:10159–10165.
   PubMed Web of Science ®Google Scholar
• Sun, L., Paulson, K. E., Schmid, C. W., Kadyk, L., and Leinwand, L. 1984. Non-Alu family interspersed repeats in human DNA and their transcriptional activity. Nucleic Acids Res. 12:2669–2690.
   PubMedGoogle Scholar
• Tautz, D., and Renz, M. 1984. Simple DNA sequences of Drosophila virilis isolated by screening with RNA. J. Mol. Biol. 172:229–235.
   PubMedGoogle Scholar
• Tu, C.-P. D., and Cohen, S. N. 1980. 3′-End labeling of DNA with [α-32P] cordycepin 5′-triphosphate. Gene 10:177–183.
   PubMed Web of Science ®Google Scholar
• Ueyama, H., Hamada, H., Battula, N., and Kakunaga, T. 1984. Structure of a human smooth muscle actin gene (aortic type) with a unique intron site. Mol. Cell. Biol. 4:1073–1078.
   PubMedGoogle Scholar
• Vandekerckhove, J., and Weber, K. 1979. The amino acid sequence of actins from bovine aorta, bovine heart, bovine fast skeletal muscle and rabbit slow skeletal muscle. Differentiation 14:124–133.
   Google Scholar
• Vasicek, T. J., McDevitt, B. E., Freeman, M. W., Fennick, B. J., Hendy, G. N., Potts, J. T., Rich, A., and Kronenberg, H. M. Nucleotide sequence of the human parathyroid hormone gene. Proc. Natl. Acad. Sci. U.S.A. 80:2127–2131.
   PubMedGoogle Scholar
• Wang, A. H. J., Quigley, G. J., Kolpack, F. J., Crawford, J. L., Van Boom, J. H., van der Marel, G., and Rich, A. 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature (London) 282:680–686.
   PubMed Web of Science ®Google Scholar
• Weintraub, H. 1983. A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin. Cell 32:1191–1203.
   PubMed Web of Science ®Google Scholar