Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Aug 1;26(15):3486–3493. doi: 10.1093/nar/26.15.3486

The Zalpha domain from human ADAR1 binds to the Z-DNA conformer of many different sequences.

A Herbert 1, M Schade 1, K Lowenhaupt 1, J Alfken 1, T Schwartz 1, L S Shlyakhtenko 1, Y L Lyubchenko 1, A Rich 1
PMCID: PMC147729  PMID: 9671809

Abstract

Z-DNA, the left-handed conformer of DNA, is stabilized by the negative supercoiling generated during the movement of an RNA polymerase through a gene. Recently, we have shown that the editing enzyme ADAR1 (double-stranded RNA adenosine deaminase, type 1) has two Z-DNA binding motifs, Zalpha and Zbeta, the function of which is currently unknown. Here we show that a peptide containing the Zalpha motif binds with high affinity to Z-DNA as a dimer, that the binding site is no larger than 6 bp and that the Zalpha domain can flip a range of sequences, including d(TA)3, into the Z-DNAconformation. Evidence is also presented to show that Zalpha and Zbeta interact to form a functional DNA binding site. Studies with atomic force microscopy reveal that binding of Zalpha to supercoiled plasmids is associated with relaxation of the plasmid. Pronounced kinking of DNA is observed, and appears to be induced by binding of Zalpha. The results reported here support a model where the Z-DNA binding motifs target ADAR1 to regions of negative supercoiling in actively transcribing genes. In this situation, binding by Zalpha would be dependent upon the local level of negative superhelicity rather than the presence of any particular sequence.

Full Text

The Full Text of this article is available as a PDF (257.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bass B. L., Nishikura K., Keller W., Seeburg P. H., Emeson R. B., O'Connell M. A., Samuel C. E., Herbert A. A standardized nomenclature for adenosine deaminases that act on RNA. RNA. 1997 Sep;3(9):947–949. [PMC free article] [PubMed] [Google Scholar]
  2. Bass B. L. RNA editing and hypermutation by adenosine deamination. Trends Biochem Sci. 1997 May;22(5):157–162. doi: 10.1016/s0968-0004(97)01035-9. [DOI] [PubMed] [Google Scholar]
  3. Binnig G, Quate CF, Gerber C. Atomic force microscope. Phys Rev Lett. 1986 Mar 3;56(9):930–933. doi: 10.1103/PhysRevLett.56.930. [DOI] [PubMed] [Google Scholar]
  4. Brennan R. G. The winged-helix DNA-binding motif: another helix-turn-helix takeoff. Cell. 1993 Sep 10;74(5):773–776. doi: 10.1016/0092-8674(93)90456-z. [DOI] [PubMed] [Google Scholar]
  5. Burns C. M., Chu H., Rueter S. M., Hutchinson L. K., Canton H., Sanders-Bush E., Emeson R. B. Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature. 1997 May 15;387(6630):303–308. doi: 10.1038/387303a0. [DOI] [PubMed] [Google Scholar]
  6. Dai Z., Dauchez M., Thomas G., Peticolas W. L. Base sequence criteria and Cartesian coordinates for stable B/Z and B/Z/B junctions in relaxed DNA. J Biomol Struct Dyn. 1992 Jun;9(6):1155–1183. doi: 10.1080/07391102.1992.10507985. [DOI] [PubMed] [Google Scholar]
  7. Egebjerg J., Kukekov V., Heinemann S. F. Intron sequence directs RNA editing of the glutamate receptor subunit GluR2 coding sequence. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10270–10274. doi: 10.1073/pnas.91.22.10270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ellison M. J., Kelleher R. J., 3rd, Wang A. H., 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 U S A. 1985 Dec;82(24):8320–8324. doi: 10.1073/pnas.82.24.8320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Haniford D. B., Pulleyblank D. E. The in-vivo occurrence of Z DNA. J Biomol Struct Dyn. 1983 Dec;1(3):593–609. doi: 10.1080/07391102.1983.10507467. [DOI] [PubMed] [Google Scholar]
  10. Hansma H. G., Hoh J. H. Biomolecular imaging with the atomic force microscope. Annu Rev Biophys Biomol Struct. 1994;23:115–139. doi: 10.1146/annurev.bb.23.060194.000555. [DOI] [PubMed] [Google Scholar]
  11. Herb A., Higuchi M., Sprengel R., Seeburg P. H. Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences. Proc Natl Acad Sci U S A. 1996 Mar 5;93(5):1875–1880. doi: 10.1073/pnas.93.5.1875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Herbert A. G., Rich A. A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide. Nucleic Acids Res. 1993 Jun 11;21(11):2669–2672. doi: 10.1093/nar/21.11.2669. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Herbert A. G., Spitzner J. R., Lowenhaupt K., Rich A. Z-DNA binding protein from chicken blood nuclei. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3339–3342. doi: 10.1073/pnas.90.8.3339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Herbert A., Alfken J., Kim Y. G., Mian I. S., Nishikura K., Rich A. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8421–8426. doi: 10.1073/pnas.94.16.8421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Herbert A., Lowenhaupt K., Spitzner J., Rich A. Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proc Natl Acad Sci U S A. 1995 Aug 1;92(16):7550–7554. doi: 10.1073/pnas.92.16.7550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Herbert A., Rich A. The biology of left-handed Z-DNA. J Biol Chem. 1996 May 17;271(20):11595–11598. doi: 10.1074/jbc.271.20.11595. [DOI] [PubMed] [Google Scholar]
  17. Higuchi M., Single F. N., Köhler M., Sommer B., Sprengel R., Seeburg P. H. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell. 1993 Dec 31;75(7):1361–1370. doi: 10.1016/0092-8674(93)90622-w. [DOI] [PubMed] [Google Scholar]
  18. 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. 1986 Oct;5(10):2737–2744. doi: 10.1002/j.1460-2075.1986.tb04558.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Köhler M., Burnashev N., Sakmann B., Seeburg P. H. Determinants of Ca2+ permeability in both TM1 and TM2 of high affinity kainate receptor channels: diversity by RNA editing. Neuron. 1993 Mar;10(3):491–500. doi: 10.1016/0896-6273(93)90336-p. [DOI] [PubMed] [Google Scholar]
  20. Kłysik J., Stirdivant S. M., Larson J. E., Hart P. A., Wells R. D. Left-handed DNA in restriction fragments and a recombinant plasmid. Nature. 1981 Apr 23;290(5808):672–677. doi: 10.1038/290672a0. [DOI] [PubMed] [Google Scholar]
  21. Liu L. F., Wang J. C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024–7027. doi: 10.1073/pnas.84.20.7024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lomeli H., Mosbacher J., Melcher T., Höger T., Geiger J. R., Kuner T., Monyer H., Higuchi M., Bach A., Seeburg P. H. Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science. 1994 Dec 9;266(5191):1709–1713. doi: 10.1126/science.7992055. [DOI] [PubMed] [Google Scholar]
  23. Lu M., Guo Q., Kallenbach N. R., Sheardy R. D. Conformational properties of B-Z junctions in DNA. Biochemistry. 1992 May 19;31(19):4712–4719. doi: 10.1021/bi00134a026. [DOI] [PubMed] [Google Scholar]
  24. Lyubchenko Y. L., Gall A. A., Shlyakhtenko L. S., Harrington R. E., Jacobs B. L., Oden P. I., Lindsay S. M. Atomic force microscopy imaging of double stranded DNA and RNA. J Biomol Struct Dyn. 1992 Dec;10(3):589–606. doi: 10.1080/07391102.1992.10508670. [DOI] [PubMed] [Google Scholar]
  25. Lyubchenko Y. L., Jacobs B. L., Lindsay S. M., Stasiak A. Atomic force microscopy of nucleoprotein complexes. Scanning Microsc. 1995 Sep;9(3):705–727. [PubMed] [Google Scholar]
  26. Lyubchenko Y. L., Oden P. I., Lampner D., Lindsay S. M., Dunker K. A. Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces. Nucleic Acids Res. 1993 Mar 11;21(5):1117–1123. doi: 10.1093/nar/21.5.1117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lyubchenko Y. L., Shlyakhtenko L. S. Visualization of supercoiled DNA with atomic force microscopy in situ. Proc Natl Acad Sci U S A. 1997 Jan 21;94(2):496–501. doi: 10.1073/pnas.94.2.496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lyubchenko Y., Shlyakhtenko L., Harrington R., Oden P., Lindsay S. Atomic force microscopy of long DNA: imaging in air and under water. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2137–2140. doi: 10.1073/pnas.90.6.2137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ma J., Qian R., Rausa F. M., 3rd, Colley K. J. Two naturally occurring alpha2,6-sialyltransferase forms with a single amino acid change in the catalytic domain differ in their catalytic activity and proteolytic processing. J Biol Chem. 1997 Jan 3;272(1):672–679. doi: 10.1074/jbc.272.1.672. [DOI] [PubMed] [Google Scholar]
  30. Peck L. J., Nordheim A., Rich A., Wang J. C. 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. 1982 Aug;79(15):4560–4564. doi: 10.1073/pnas.79.15.4560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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. 1972 Jun 28;67(3):375–396. doi: 10.1016/0022-2836(72)90457-3. [DOI] [PubMed] [Google Scholar]
  32. Polson A. G., Bass B. L. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 1994 Dec 1;13(23):5701–5711. doi: 10.1002/j.1460-2075.1994.tb06908.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Rahmouni A. R., Wells R. D. Stabilization of Z DNA in vivo by localized supercoiling. Science. 1989 Oct 20;246(4928):358–363. doi: 10.1126/science.2678475. [DOI] [PubMed] [Google Scholar]
  34. Ridoux J. P., Liquier J., Taillandier E. Raman spectroscopy of Z-form poly[d(A-T)].poly[d(A-T)]. Biochemistry. 1988 May 17;27(10):3874–3878. doi: 10.1021/bi00410a052. [DOI] [PubMed] [Google Scholar]
  35. Seeman N. C., Rosenberg J. M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. doi: 10.1073/pnas.73.3.804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Shlyakhtenko L. S., Potaman V. N., Sinden R. R., Lyubchenko Y. L. Structure and dynamics of supercoil-stabilized DNA cruciforms. J Mol Biol. 1998 Jul 3;280(1):61–72. doi: 10.1006/jmbi.1998.1855. [DOI] [PubMed] [Google Scholar]
  37. Smith H. C., Gott J. M., Hanson M. R. A guide to RNA editing. RNA. 1997 Oct;3(10):1105–1123. [PMC free article] [PubMed] [Google Scholar]
  38. Sommer B., Köhler M., Sprengel R., Seeburg P. H. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell. 1991 Oct 4;67(1):11–19. doi: 10.1016/0092-8674(91)90568-j. [DOI] [PubMed] [Google Scholar]
  39. Wang A. H., Hakoshima T., van der Marel G., van Boom J. H., Rich A. AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG). Cell. 1984 May;37(1):321–331. doi: 10.1016/0092-8674(84)90328-3. [DOI] [PubMed] [Google Scholar]
  40. Wittig B., Wölfl 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. 1992 Dec;11(12):4653–4663. doi: 10.1002/j.1460-2075.1992.tb05567.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Wölfl 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 U S A. 1996 Apr 16;93(8):3664–3668. doi: 10.1073/pnas.93.8.3664. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES