As of 1 April 2026, the PSJD database will become an archive and will no longer accept new data. Current publications from Polish scientific journals are available through the Library of Science: https://bibliotekanauki.pl
The conversion of right-handed dsDNA and dsRNA to the left-handed Z-conformation involves a reorganization of the nucleotides relative to each other. This conversion can be facilitated by the tight binding of a Z-conformation-specific protein domain from the editing enzyme dsRNA adenosine deaminase. This may influence the modification of both pre-mRNAs as well as some replicating RNA viruses.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A.
References
1. Rich, A. (1993) DNA comes in many forms. Gene 135, 99-109.
2. Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G. & Rich, A. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680-686.
3. Klysik, J., Stirdivant, S.M., Larson, J.E., Hart, P.A. & Wells, R.D. (1981) Left-handed DNA in restriction fragments and a recombinant plasmid. Nature 290, 672-677.
4. Haniford, D.B. & Pulleyblank, D.E. (1983) Facile transition of poly[d(TG)·d(CA)] into a left-handed helix in physiological conditions. Nature 302, 632-634.
5. Peck, L.J., Nordheim, A., Rich, A. & 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.
6. Pohl, F.M. & Jovin, T.M. (1972) Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly (dG-dC). J. Mol. Biol. 67, 375-396.
7. Behe, M. & Felsenfeld, G. (1981) Effects of methylation on a synthetic polynucleotide: The B-Z transition in poly(dG-m5dC)· poly(dG-m5dC). Proc. Natl. Acad. Sci. U.S.A. 78, 1619-1623.
8. Singleton, C.K., Klysik, J., Stirdivant, S.M. & Wells, R.D. (1982) Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature 299, 312-316.
9. Peck, L.J. & Wang, J.C. (1983) Energetics of B-to-Z transition in DNA. Proc. Natl. Acad. Sci. U.S.A. 80, 6206-6210.
10. Ellison, M.J., Kelleher, R.J. 3rd., Wang, A.H.-J., Habener, J.F. & Rich, A. (1985) Sequence-dependent energetics of the B-Z transition in supercoiled DNA containing nonalternating purine-pyrimidine sequences. Proc. Natl. Acad. Sci. U.S.A. 82, 8320-8324.
11. McLean, M.J., Blaho, J.A., Kilpatrick, M.W. & Wells, R.D. (1986) Consecutive A · T pairs can adopt a left-handed DNA structure. Proc. Natl. Acad. Sci. U.S.A. 83, 5884-5888.
12. Ellison, M.J., Feigon, J., Kelleher, R.J. 3rd., Wang, A.H.-J., Habener, J.F. & Rich, A. (1986) An assessment of the Z-DNA forming potential of alternating dA-dT stretches in supercoiled plasmids. Biochemistry 25, 3648-3655.
13. Ho, P.S., Ellison, M.J., Quigley, G.J. & Rich, A. (1986) A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J. 5, 2737-2744.
14. Liu, L.F. & Wang, J.C. (1987) Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. U.S.A. 84, 7024-7027.
15. Schroth, G.P., Chou, P.J. & Ho, P.S. (1992) Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J. Biol. Chem. 267, 11846-11855.
16. Palecek, E., Rasovska, E. & Boublikova, P. (1988) Probing of DNA polymorphic structure in the cell with osmium tetroxide. Biochem. Biophys. Res. Commun. 150, 731-738.
17. Zheng, G.X., Kochel, T., Hoepfner, R.W., Timmons, S.E. & Sinden, R.R. (1991) Torsionally tuned cruciform and Z-DNA probes for measuring unrestrained supercoiling at specific sites in DNA of living cells. J. Mol. Biol. 221, 107-122.
18. Jaworski, A., Hsieh, W.-T., Blaho, J.A., Larson, J.E. & Wells, R.D. (1987) Left-handed DNA in vivo. Science 238, 773-777.
19. Rahmouni, A.R. & Wells, R.D. (1989) Stabilization of Z DNA in vivo by localized supercoiling. Science 246, 358-363.
20. Jaworski, A., Higgins, N.P., Wells, R.D. & Zacharias, W. (1991) Topoisomerase mutants and physiological conditions control supercoiling and Z-DNA formation in vivo. J. Biol. Chem. 266, 2576-2581.
21. Krasilnikov, A.S., Podtelezhnikov, A., Vologodskii, A. & Mirkin, S.M. (1999) Large- scale effects of transcriptional DNA supercoiling in vivo. J. Mol. Biol. 292, 1149-1160.
22. Lafer, E.M., Moller, A., Nordheim, A., Stollar, B.D. & Rich, A. (1981) Antibodies specific for left-handed Z-DNA. Proc. Natl. Acad. Sci. U.S.A. 78, 3546-3550.
23. Lafer, E.M., Valle, R.P., Moller, A., Nordheim, A., Schur, P.H., Rich, A. & Stollar, B.D. (1983) Z-DNA-specific antibodies in human systemic lupus erythematosus. J. Clin. Invest. 71, 314-321.
24. Nordheim, A., Pardue, M.L., Lafer, E.M., Moller, A., Stollar, B.D. & Rich, A. (1981) Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature 294, 417-422.
25. Lancillotti, F., Lopez, M.C., Arias, P. & Alonso, C. (1987) Z-DNA in transcriptionally active chromosomes. Proc. Natl. Acad. Sci. U.S.A. 84, 1560-1564.
26. Hill, R.J. (1991) Z-DNA: A prodrome for the 1990s. J. Cell Sci. 99, 675-680.
27. Lipps, H.J., Nordheim, A., Lafer, E. M., Ammermann, D., Stollar, B.D. & Rich, A. (1983) Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate Stylonychia mytilus. Cell 32, 435-441.
28. Gruskin, E.A. & Rich, A. (1993) B-DNA to Z-DNA structural transitions in the SV40 enhancer: Stabilization of Z-DNA in negatively supercoiled DNA minicircles. Biochemistry 32, 2167-2176.
29. Jackson, D.A. & Cook, P.R. (1985) A general method for preparing chromatin containing intact DNA. EMBO J. 4, 913-918.
30. Jackson, D.A., Yuan, J. & Cook, P.R. (1988) A gentle method for preparing cyto- and nucleo- skeletons and associated chromatin. J. Cell Sci. 90, 365-378.
31. Wittig, B., Dorbic, T. & Rich, A. (1989) The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain. J. Cell Biol.108, 755-764.
32. Wittig, B., Dorbic, T. & Rich, A. (1991) Transcription is associated with Z-DNA formation in metabolically active permeabilized mammalian cell nuclei. Proc. Natl. Acad. Sci. U.S.A. 88, 2259-2263.
33. Wittig, B., Wolfl, S., Dorbic, T., Vahrson, W. & Rich, A. (1992) 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.
34. Wolfl, S., Wittig, B. & Rich, A. (1995) Identification of transcriptionally induced Z-DNA segments in the human c-myc gene. Biochim. Biophys. Acta 1264, 294-302.
35. Wolfl, S., Martinez, C., Rich, A. & Majzoub, J.A. (1996) Transcription of the human corticotropin-releasing hormone gene in NPLC cells is correlated with Z-DNA formation. Proc. Natl. Acad. Sci. U.S.A. 93, 3664-3668.
36. Peck, L.J. & Wang, J.C. (1985) Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence. Cell 40, 129-137.
37. Rich, A. (1994) Speculation on the biological roles of left-handed Z-DNA. Ann. NY Acad. Sci. 726, 1-16; discussion 16-17.
38. Pohl, F.M. (1967) [A model of the DNA structure]. Naturwissenschaften 54, 616.
39. Treco, D. & Arnheim, N. (1986) The evolutionarily conserved repetitive sequence d(TG·AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis. Mol. Cell. Biol. 6, 3934- 3947.
40. Bullock, P., Miller, J. & Botchan, M. (1986) Effects of poly[d(pGpT)·d(pApC)] and poly[d(pCpG) · d(pCpG)] repeats on homologous recombination in somatic cells. Mol. Cell. Biol. 6, 3948-3953.
41. Wahls, W.P., Wallace, L.J. & Moore, P.D. (1990) The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture. Mol. Cell. Biol. 10, 785-793.
42. Garner, M.M. & Felsenfeld, G. (1987) Effect of Z-DNA on nucleosome placement. J. Mol. Biol. 196, 581-590.
43. Wolfl, S., Vahrson, W. & Herbert, A.G. (1995) Analysis of left-handed Z-DNA in vivo; in DNA and Nucleoprotein Structure in vivo (Salus, H.P. & Wiebauer, K., eds.) pp. 137-159, R.G. Landes Co., Austin.
44. Krishna, P., Kennedy, B.P., Waisman, D.M., van de Sande, J.H. & McGhee, J.D. (1990) Are many Z-DNA binding proteins actually phospholipid-binding proteins? Proc. Natl. Acad. Sci. U.S.A. 87, 1292-1295.
45. Rohner, K.J., Hobi, R. & Kuenzle, C.C. (1990) Z-DNA-binding proteins. Identification critically depends on the proper choice of ligands. J. Biol. Chem. 265, 19112-19115.
46. Herbert, A., Lowenhaupt, K., Spitzner, J. & Rich, A. (1995) Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proc. Natl. Acad. Sci. U.S.A. 92, 7550-7554.
47. Schwartz, T., Lowenhaupt, K., Kim, Y.-G., Li, L., Brown, B.A., 2nd, Herbert, A. & Rich, A. (1999) Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1. J. Biol. Chem. 274, 2899-2906.
48. Herbert, A.G., Spitzner, J.R., Lowenhaupt, K. & Rich, A. (1993) Z-DNA binding protein from chicken blood nuclei. Proc. Natl. Acad. Sci. U.S.A. 90, 3339-3342.
49. Herbert, A., Alfken, J., Kim, Y.G., Mian, I.S., Nishikura, K. & Rich, A. (1997) A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl. Acad. Sci. U.S.A. 94, 8421- 8426.
50. Herbert, A., Schade, M., Lowenhaupt, K., Alfken, J., Schwartz, T., Shlyakhtenko, L.S., Lyubchenko, Y.L. & Rich, A. (1998) The Zα domain from human ADAR1 binds to the Z-DNA conformer of many different sequences. Nucleic Acids Res. 26, 3486-3493.
51. Schade, M., Behlke, J., Lowenhaupt, K., Herbert, A., Rich, A. & Oschkinat, H. (1999) A 6 bp Z-DNA hairpin binds two Zα domains from the human RNA editing enzyme ADAR1. FEBS Lett. 458, 27-31.
52. Melcher, T., Maas, S., Herb, A., Sprengel, R., Seeburg, P.H. & Higuchi, M. (1996) A mammalian RNA editing enzyme. Nature 379, 460- 464.
53. Bass, B.L. (1993) RNA editing: New uses for old players in the RNA world; in The RNA World (Gesteland, R.F. & Atkins, J.F., eds.) pp. 383-418, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
54. Wagner, R.W. & Nishikura, K. (1988) Cell cycle expression of RNA duplex unwindase activity in mammalian cells. Mol. Cell. Biol. 8, 770-777.
55. Herbert, A. (1996) RNA editing, introns and evolution. Trends Genet 12, 6-9.
56. Maas, S. & Rich, A. (2000) Changing genetic information through RNA editing. Bioessays 22, 790-802.
57. Sommer, B., Kohler, M., Sprengel, R. & Seeburg, P.H. (1991) RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 67, 11-19.
58. Lomeli, H., Mosbacher, J., Melcher, T., Hoger, T., Geiger, J.R., Kuner, T., Monyer, H., Higuchi, M., Bach, A. & Seeburg, P.H. (1994) Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science 266, 1709-1713.
59. Burns, C.M., Chu, H., Rueter, S.M., Hutchinson, L.K., Canton, H., Sanders-Bush, E. & Emeson, R.B. (1997) Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature 387, 303-308.
60. Ma, J., Qian, R., Rausa, F.M., 3rd, & Colley, K.J. (1997) Two naturally occurring α2,6-sialyltransferase forms with a single amino acid change in the catalytic domain differ in their catalytic activity and proteolytic processing. J. Biol. Chem. 272, 672-679.
61. Kask, K., Zamanillo, D., Rozov, A., Burnashev, N., Sprengel, R. & Seeburg, P.H. (1998) The AMPA receptor subunit GluR-B in its Q/R site-unedited form is not essential for brain development and function. Proc. Natl. Acad. Sci. U.S.A. 95, 13777-13782.
62. Higuchi, M., Single, F.N., Kohler, M., Sommer, B., Sprengel, R. & Seeburg, P.H. (1993) RNA editing of AMPA receptor subunit GluR-B: A base-paired intron-exon structure determines position and efficiency. Cell 75, 1361-1370.
63. Schwartz, T., Shafer, K., Lowenhaupt, K., Hanlon, E., Herbert, A. & Rich, A. (1999) Crystallization and preliminary studies of the DNA-binding domain Zα from ADAR1 complexed to left-handed DNA. Acta Crystallogr. D Biol. Crystallogr. 55, 1362-1364.
64. Schwartz, T., Rould, M.A., Lowenhaupt, K., Herbert, A. & Rich, A. (1999) Crystal structure of the Zα domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284, 1841-1845.
65. Patterson, J.B. & Samuel, C.E. (1995) Expression and regulation by interferon of a double-stranded RNA-specific adenosine deaminase from human cells: Evidence for two forms of the deaminase. Mol. Cell. Biol. 15, 5376-5388.
66. Cattaneo, R. & Billeter, M.A. (1992) Mutations and A/I hypermutations in measles virus persistent infections. Curr. Top. Microbiol. Immunol. 176, 63-74.
67. Cattaneo, R. (1994) Biased (A→I) hypermutation of animal RNA virus genomes. Curr. Opin. Genet. Dev. 4, 895-900.
68. Bass, B.L. (1997) RNA editing and hypermutation by adenosine deamination. Trends Biochem. Sci. 22, 157-162.
69. Jacobs, B.L. & Langland, J.O. (1996) When two strands are better than one: The mediators and modulators of the cellular responses to double-stranded RNA. Virology 219, 339- 349.
70. Hall, K., Cruz, P., Tinoco, I., Jr., Jovin, T.M. & van de Sande, J.H. (1984) 'Z-RNA'-a left-handed RNA double helix. Nature 311, 584-586.
71. Teng, M.K., Liaw, Y.C., van der Marel, G.A., van Boom, J.H. & Wang, A.H. (1989) Effects of the O2' hydroxyl group on Z-DNA conformation: Structure of Z-RNA and (araC)- [Z-DNA]. Biochemistry 28, 4923-4928.
72. Davis, P.W., Adamiak, R.W. & Tinoco, I., Jr. (1990) Z-RNA: The solution NMR structure of r(CGCGCG). Biopolymers 29, 109-122.
73. Tinoco, I., Jr., Cruz, P., Davis, P.W., Hall, K., Hardin, C.C., Mathies, R.A., Puglisi, J.D., Trulson, M.O., Johnson, W.C., Jr. & Neilson, T. (1986) Z-RNA: A left-handed double helix; in Structure and Dynamics of RNA (van Knippenberg, P.H. & Hilbers, C.W., eds.) pp. 55-66, Plenum, New York.
74. Klump, H.H. & Jovin, T.M. (1987) Formation of a left-handed RNA double helix: Energetics of the A-Z transition of poly[r(G-C)] in concentrated NaClO4 solutions. Biochemistry 26, 5186-5190.
75. Olson, W.K. & Sussman, J.L. (1982) How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies. J. Am. Chem. Soc. 104, 207-278.
76. Sanger, W. (1984) Principles of Nucleic Acid Structure; in Springer Advanced Texts in Chemistry (Cantor, C. R., ed.) Springer-Verlag, New York.
77. Brown, B.A., 2nd, Lowenhaupt, K., Wilbert, C.M., Hanlon, E. & Rich, A. (2000) The Zα domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc. Natl. Acad. Sci. U.S.A. 97, 13532-13536.
79. Wang, A.J., Quigley, G.J., Kolpak, F.J., van der Marel, G., van Boom, J.H. & Rich, A. (1981) Left-handed double helical DNA: Variations in the backbone conformation. Science 211, 171-176.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv48i2p295kz
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.