References
Wang, A. H. J. et al. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680–686 (1979).
Pohl, F. M. & Jovin, T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). J. Mol. Biol. 67, 375–396 (1972).
Thamann, T. J., Lord, R. C., Wang, A. H. J. & Rich, A. High salt form of poly(dG-dC)·poly(dG-dC) is left handed Z-DNA: raman spectra of crystals and solutions. Nucl. Acids Res. 9, 5443–5457 (1981).
Behe, M. & Felsenfeld, G. Effects of methylation on a synthetic polynucleotide: the B–Z transition in poly(dG–m5dC)·poly(dG–m5dC). Proc. Natl Acad. Sci. USA 78, 1619–1623 (1981).
Rich, A., Nordheim, A. & Wang, A. H. -J. The chemistry and biology of left-handed Z-DNA. Ann. Rev. Biochem. 53, 791–846 (1984).
Nordheim, A. & Rich, A. The sequence (dC–dA)n·(dG–dT)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc. Natl Acad. Sci. USA 80, 1821–1825 (1983).
Haniford, D. B. & Pulleyblank, D. E. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature 302, 632–634 (1983).
Feigon, J., Wang, A. H. -J., van der Marel, G. A., van Boom, J. H. & Rich, A. Z-DNA forms without an alternating purine–pyrimidine sequence in solution. Science 230, 82–84 (1985).
Peck, L. J., Nordheim, A., Rich, A. & Wang, J. C. Flipping of cloned d(pGpG)n·d(pCpG)n DNA sequences from right to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc. Natl Acad. Sci. USA 79, 4560–4564 (1982).
Haniford, D. B. & Pulleyblank, D. E. The in vivo occurrence of Z-DNA. J. Biomol. Struct. Dyn. 1, 593–609 (1983).
Ellison, M. J., Kelleher, R. J., Wang, A. H. -J., Habener, J. F. & Rich, A. Sequence-dependent energetics of the B–Z transition in supercoiled DNA containing nonalternating purine–pyrimidine sequences. Proc. Natl Acad. Sci. USA 82, 8320–8324 (1985).
Ho, P. S., Ellison, M. J., Quigley, G. J. & Rich, A. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J. 5, 2737–2744 (1986).
Marx, J. Z-DNA: still searching for a function. Science 230, 794–796 (1985).
Lafer, E. M., Moller, A., Nordheim, A., Stollar, B. D. & Rich, A. Antibodies specific for left-handed DNA. Proc. Natl Acad. Sci. USA 78, 3546–3550 (1981).
Moller, A. et al. Monoclonal antibodies recognize different parts of Z-DNA. J. Biol. Chem. 257, 12081–12085 (1982).
CAS PubMed Google Scholar
Lafer, E. M. et al. Z-DNA specific antibodies in human systemic lupus erythematosus. J. Clin. Invest. 71, 314–321 (1983).
Nordheim, A. et al. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature 294, 417–422 (1981).
Lancillotti, F., Lopez, M. C., Arias, P. & Alonso, C. Z-DNA in transcriptionally active chromosomes. Proc. Natl Acad. Sci. USA 84, 1560–1564 (1987).
Arndt-Jovin, D. J. et al. Left-handed Z-DNA in bands of acid-fixed polytene chromosomes. Proc. Natl Acad. Sci. USA 80, 4344–4348 (1983).
Lipps, H. J. et al. Antibodies against Z-DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate Stylonychia mytilus. Cell 32, 435–441 (1983).
Liu, L. F. & Wang, J. C. Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. USA 84, 7024–7027 (1987).
Schroth, G. P., Chou, P. -J. & Ho, P. S. Mapping Z-DNA in the human genome: computer aided mapping reveals a non-random distribution of potential Z-DNA forming sequences in human genes. J. Biol. Chem. 267, 11846–11855 (1992).
CAS PubMed Google Scholar
Jackson, D. A., Yuan, J. & Cook, P. R. A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. J. Cell Sci. 90, 365–378 (1988).
CAS PubMed Google Scholar
Wittig, B., Dorbic, T. & Rich, A. The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain. J. Cell. Biol. 108, 755–764 (1989).
Wittig, B., Dorbic, T. & Rich, A. Transcription is associated with Z-DNA formation in metabolically active permeabilized mammalian cell nuclei. Proc. Natl Acad. Sci. USA 88, 2259–2263 (1991).
Wittig, B., Wolfl, S., Dorbic, T., Vahrson, W. & Rich, A. Transcription of human C-MYC in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene. EMBO J. 11, 4653–4663 (1992).
Wolfl, S., Wittig, B. & Rich, A. Identification of transcriptionally induced Z-DNA segments in the human C-MYC gene. Biochim. Biophys. Acta 1264, 294–302 (1995).
Wolfl, S., Martinez, C., Rich, A. & Majzoub, J. A. Transcription of the human corticotropin-releasing hormone gene in NPLC cells is correlated with Z-DNA formation. Proc. Natl Acad. Sci. USA 93, 3664–3668 (1996).
Liu, R. et al. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell 106, 309–318 (2001).
Garner, M. M. & Felsenfeld, G. Effect of Z-DNA on nucleosome placement. J. Mol. Biol. 196, 581–590 (1987).
Herbert, A. G. & Rich, A. A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide. Nucl. Acids Res. 21, 2669–2672 (1993).
Herbert, A., Lowenhaupt, K., Spitzner, J. & Rich, A. Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proc. Natl Acad. Sci. USA 92, 7550–7554 (1995).
Bass, B. L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817–846 (2002).
Herbert, A. et al. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl Acad. Sci. USA 94, 8421–8426 (1997).
Kim, Y. -G., Kim, P. S., Herbert, A. & Rich, A. Construction of a Z-DNA-specific restriction endonuclease. Proc. Natl Acad. Sci. USA 94, 12875–12879 (1997).
Kim, Y. G., Lowenhaupt, K., Schwartz, T. & Rich, A. The interaction between Z-DNA and the Zab domain of dsRNA adenosine deaminase characterized using fusion nucleases. J. Biol. Chem. 274, 19081–19086 (1999).
Berger, I. et al. Spectroscopic characterization of a DNA-binding domain, Zα, from the editing enzyme dsRNA adenosine deaminase: evidence for left-handed Z-DNA in the Zα-DNA complex. Biochemistry 37, 13313–13321 (1998).
Kim, Y. -G. et al. The Zab domain of the human RNA editing enzyme ADAR1 recognizes Z-DNA when surrounded by B-DNA. J. Biol. Chem. 275, 26828–26833 (2000).
CAS PubMed Google Scholar
Oh, D. -B., Kim, Y. -G. & Rich, A. Z-DNA-binding proteins can act as potent effectors of gene expression in vivo. Proc. Natl Acad. Sci. USA 99, 16666–16671 (2002).
Schwartz, T., Rould, M. A., Lowenhaupt, K., Herbert, A. & Rich, A. Crystal structure of the Zα domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284, 1841–1845 (1999).
Herbert, A. & Rich, A. Role of binding domains for dsRNA and Z-DNA in the in vivo editing of minimal substrates by ADAR1. Proc. Natl Acad. Sci. USA 98, 12132–12137 (2001).
Fu, Y. et al. Cloning of DLM-1, a novel gene that is up-regulated in activated macrophages, using RNA differential display. Gene 240, 157–163 (1999).
Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U. & Rich, A. Structure of the DLM-1–Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nature Struct. Biol. 8, 761–765 (2001).
Brandt, T. A. & Jacobs, B. L. Both carboxy- and amino-terminal domains of the vaccinia virus interferon resistance gene, E3L are required for pathogenesis in a mouse model. J. Virol. 75, 850–856 (2001).
Kim, Y. -G. et al. A role for Z-DNA binding in vaccinia virus pathogenesis. Proc. Natl Acad. Sci. USA 100, 6974–6979 (2003).
Zhang, S., Lockshin, C., Herbert, A., Winter, E. & Rich, A. Zuotin, a putative Z-DNA binding protein in Saccharomyces cerevisiae. EMBO J. 11, 3787–3796 (1992).
Zhang, S., Holmes, T., Lockshin, C. & Rich, A. Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane. Proc. Natl Acad. Sci. USA 90, 3334–3338 (1993).
Zhang, S. et al. Self-complementary oligopeptide matrices support mammalian cell attachment. Biomaterials 16, 1385–1393 (1995).
Holmes, T., Delacalle, S., Su, X., Rich, A. & Zhang, S. Extensive neurite outgrowth and active neuronal synapses on peptide scaffolds. Proc. Natl Acad. Sci. USA 97, 6728–6733 (2000).
Kisiday, J. et al. Self-assembling peptide hydrogel fosters chondrocyte extracellular matrix production and cell division: implications for cartilage tissue repair. Proc. Natl Acad. Sci. USA 99, 9996–10001 (2002).
Zhang, S. & Rich, A. Direct conversion of an oligopeptide from a β-sheet to an α-helix: a model for amyloid formation. Proc. Natl Acad. Sci. USA 94, 23–28 (1997).
Zhang, S. et al. Biological surface engineering: a simple system for cell pattern formation. Biomaterials 20, 1213–1220 (1999).
Vauthey, S., Santoso, S., Gong, H., Watson, N. & Zhang, S. Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles. Proc. Natl Acad. Sci. USA 99, 5355–5360 (2002).
von Maltzahn, G., Vauthey, S., Santoso, S. & Zhang, S. Positively charged surfactant-like peptides self-assemble into nanostructures. Langmuir 19, 4332–4337 (2003).
Zhang, S. Building from bottom-up. Materials Today 6, 20–27 (2003).
Uesugi, W., Shida, T. & Ikehara, M. Synthesis and properties of CpG analogues containing an 8-bromoguanosine residue. Evidence for Z-RNA duplex formation. Biochemistry 21, 3400–3408 (1982).
Hall, K., Cruz, P., Tinoko, I., Jovin, T. M. & van de Sande, J. H. 'Z-RNA' — a left-handed RNA double helix. Nature 311, 584–586 (1984).
Davis, P. W., Hall, K., Cruz, P., Tinoco, I. & Neilson, T. The tetraribonucleotide rCpGpCpG forms a left-handed Z-RNA double helix. Nucleic Acids Res. 14, 1279–1291 (1986).
Teng, M. K., Liaw, Y. C., van der Marel, G. A., van Boom, J. H. & Wang, A. -H. Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]. Biochemistry 28, 4923–4928 (1989).
Davis, P. W., Adamiak, R. W. & Tinoco, I. Z-RNA: the solution NMR structure of r(CGCGCG). Biopolymers 29, 109–122 (1990).
Hardin, C. C., Zarling, D. A., Wolk, S. K., Ross, W. S. & Tincoc, I. Characterization of anti-Z-RNA polyclonal antibodies: epitope properties and recognition of Z-DNA. Biochemistry 27, 4169–4177 (1988).
Zarling, D. A., Calhoun, C. J., Hardin, C. C. & Zarling, A. H. Cytoplasmic Z-RNA. Proc. Natl Acad. Sci. USA 84, 6117–6121 (1987).
Zarling, D. A., Calhoun, C. J., Feuerstein, B. G. & Sena, E. P. Cytoplasmic microinjection of immunoglobulin Gs recognizing RNA helices inhibits human cell growth. J. Mol. Biol. 211, 147–160 (1990).
Brown, B. A., Lowenhaupt, K., Wilbert, C. M., Hanlon, C. B. & Rich, A. The Za domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc. Natl Acad. Sci. USA 97, 13532–13586 (2000).