Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 May 25;17(10):3795–3810. doi: 10.1093/nar/17.10.3795

Direct evidence for the presence of left-handed conformation in a supramolecular assembly of polynucleotides.

T J Thomas 1, T Thomas 1
PMCID: PMC317860  PMID: 2660102

Abstract

Hexammine cobalt(III) chloride (Co(NH3)6(3+) provokes a B-DNA----Z-DNA----psi-DNA conformational transition in poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC). The circular dichroism spectrum of psi-DNA is characterized by a manyfold increase of positive ellipticity in the range of 300-225 nm and the complete absence of a negative peak. In order to ascertain the helical handedness of psi-DNA, we used a recently developed enzyme immunoassay technique. This method consisted of treating the polynucleotides with Co(NH3)6(3+) to convert them to the Z- or psi-DNA forms and immobilizing these conformations on a microtiter plate. The plates were subsequently treated with a monoclonal anti-Z-DNA antibody Z22, alkaline phosphatase conjugated, affinity purified immunoglobulins, and the phosphatase substrate. The enzyme-substrate reaction was monitored by reading the absorbance at 405 nm with a microplate autoreader. The monoclonal anti-Z-DNA antibody had no reactivity to the B-DNA form, but bound strongly to both the Z- and psi-DNA forms, showing that Co(NH3)6(3+)-induced psi-DNA form of the polynucleotides exists in the left-handed Z-DNA conformation.

Full text

PDF
3795

Selected References

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

  1. Basu H. S., Marton L. J. The interaction of spermine and pentamines with DNA. Biochem J. 1987 May 15;244(1):243–246. doi: 10.1042/bj2440243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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 U S A. 1981 Mar;78(3):1619–1623. doi: 10.1073/pnas.78.3.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Damaschun H., Damaschun G., Becker M., Buder E., Misselwitz R., Zirwer D. Study of DNA-spermine interactions by use of small-angle and wide-angle X-ray scattering and circular dichroism. Nucleic Acids Res. 1978 Oct;5(10):3801–3809. doi: 10.1093/nar/5.10.3801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Eaton R. B., Schnneider G., Schur P. H. Enzyme immunoassay for antibodies to native DNA. Specificity and quality of antibodies. Arthritis Rheum. 1983 Jan;26(1):52–62. doi: 10.1002/art.1780260109. [DOI] [PubMed] [Google Scholar]
  5. Eichhorn G. L., Shin Y. A., Butzow J. J. Transitions induced by metal complexes among several forms of DNA. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):125–127. doi: 10.1101/sqb.1983.047.01.016. [DOI] [PubMed] [Google Scholar]
  6. Eickbush T. H., Moudrianakis E. N. The compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroids. Cell. 1978 Feb;13(2):295–306. doi: 10.1016/0092-8674(78)90198-8. [DOI] [PubMed] [Google Scholar]
  7. Gessner R. V., Quigley G. J., Wang A. H., van der Marel G. A., van Boom J. H., Rich A. Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations. Biochemistry. 1985 Jan 15;24(2):237–240. doi: 10.1021/bi00323a001. [DOI] [PubMed] [Google Scholar]
  8. Gosule L. C., Schellman J. A. Compact form of DNA induced by spermidine. Nature. 1976 Jan 29;259(5541):333–335. doi: 10.1038/259333a0. [DOI] [PubMed] [Google Scholar]
  9. Haniford D. B., Pulleyblank D. E. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature. 1983 Apr 14;302(5909):632–634. doi: 10.1038/302632a0. [DOI] [PubMed] [Google Scholar]
  10. Hingerty B. E., Brown R. S., Klug A. Stabilization of the tertiary structure of yeast phenylalanine tRNA by [Co(NH3)6]3+. X-ray evidence for hydrogen bonding to pairs of guanine bases in the major groove. Biochim Biophys Acta. 1982 Apr 26;697(1):78–82. doi: 10.1016/0167-4781(82)90047-1. [DOI] [PubMed] [Google Scholar]
  11. Jordan C. F., Lerman L. S., Venable J. H. Structure and circular dichroism of DNA in concentrated polymer solutions. Nat New Biol. 1972 Mar 22;236(64):67–70. doi: 10.1038/newbio236067a0. [DOI] [PubMed] [Google Scholar]
  12. Lafer E. M., Möller A., Nordheim A., Stollar B. D., Rich A. Antibodies specific for left-handed Z-DNA. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3546–3550. doi: 10.1073/pnas.78.6.3546. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Maestre M. F., Reich C. Contribution of light scattering to the circular dichroism of deoxyribonucleic acid films, deoxyribonucleic acid-polylysine complexes, and deoxyribonucleic acid particles in ethanolic buffers. Biochemistry. 1980 Nov 11;19(23):5214–5223. doi: 10.1021/bi00564a010. [DOI] [PubMed] [Google Scholar]
  14. Möller A., Gabriels J. E., Lafer E. M., Nordheim A., Rich A., Stollar B. D. Monoclonal antibodies recognize different parts of Z-DNA. J Biol Chem. 1982 Oct 25;257(20):12081–12085. [PubMed] [Google Scholar]
  15. Nickol J., Behe M., Felsenfeld G. Effect of the B--Z transition in poly(dG-m5dC) . poly(dG-m5dC) on nucleosome formation. Proc Natl Acad Sci U S A. 1982 Mar;79(6):1771–1775. doi: 10.1073/pnas.79.6.1771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nordheim A., Lafer E. M., Peck L. J., Wang J. C., Stollar B. D., Rich A. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell. 1982 Dec;31(2 Pt 1):309–318. doi: 10.1016/0092-8674(82)90124-6. [DOI] [PubMed] [Google Scholar]
  17. Nordheim A., Pardue M. L., Weiner L. M., Lowenhaupt K., Scholten P., Möller A., Rich A., Stollar B. D. Analysis of Z-DNA in fixed polytene chromosomes with monoclonal antibodies that show base sequence-dependent selectivity in reactions with supercoiled plasmids and polynucleotides. J Biol Chem. 1986 Jan 5;261(1):468–476. [PubMed] [Google Scholar]
  18. Nordheim A., Rich A. The sequence (dC-dA)n X (dG-dT)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc Natl Acad Sci U S A. 1983 Apr;80(7):1821–1825. doi: 10.1073/pnas.80.7.1821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. 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]
  21. Revet B., Delain E., Dante R., Niveleau A. Three dimensional association of double-stranded helices are produced in conditions for Z-DNA formation. J Biomol Struct Dyn. 1983 Dec;1(4):857–871. doi: 10.1080/07391102.1983.10507489. [DOI] [PubMed] [Google Scholar]
  22. Shin Y. A., Butzow J. J., Sinsel L. D., Clark P., Pillai R. P., Johnson W. C., Eichhorn G. L. Metal-induced sequential transitions among DNA conformations. Biopolymers. 1988 Sep;27(9):1415–1432. doi: 10.1002/bip.360270908. [DOI] [PubMed] [Google Scholar]
  23. Shin Y. A., Eichhorn G. L. Formation of psi (+) and psi (-) DNA. Biopolymers. 1984 Feb;23(2):325–335. doi: 10.1002/bip.360230211. [DOI] [PubMed] [Google Scholar]
  24. Shin Y. A., Eichhorn G. L. Reversible change in psi structure of DNA-poly(Lys) complexes induced by metal binding. Biopolymers. 1977 Jan;16(1):225–230. doi: 10.1002/bip.1977.360160117. [DOI] [PubMed] [Google Scholar]
  25. Thomas T. J., Baarsch M. J., Messner R. P. Immunological detection of B-DNA to Z-DNA transition of polynucleotides by immobilization of the DNA conformation on a solid support. Anal Biochem. 1988 Feb 1;168(2):358–366. doi: 10.1016/0003-2697(88)90330-2. [DOI] [PubMed] [Google Scholar]
  26. Thomas T. J., Bloomfield V. A., Canellakis Z. N. Differential effects on the B-to-Z transition of poly(dG-me5dC).poly(dG-me5dC) produced by N1- and N8-acetyl spermidine. Biopolymers. 1985 Apr;24(4):725–729. doi: 10.1002/bip.360240411. [DOI] [PubMed] [Google Scholar]
  27. Thomas T. J., Bloomfield V. A. Toroidal condensation of Z DNA and identification of an intermediate in the B to Z transition of poly(dG-m5dC) X poly(dG-m5dC). Biochemistry. 1985 Jan 29;24(3):713–719. doi: 10.1021/bi00324a026. [DOI] [PubMed] [Google Scholar]
  28. Thomas T. J., Messner R. P. A left-handed (Z) conformation of poly(dA-dC).poly(dG-dT) induced by polyamines. Nucleic Acids Res. 1986 Aug 26;14(16):6721–6733. doi: 10.1093/nar/14.16.6721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Thomas T. J., Messner R. P. Hexammineruthenium (III) chloride: a highly efficient promoter of the B-DNA to Z-DNA transition of poly-(dG-m5dC).poly(dG-m5dC) and poly(dG-dC).poly(dG-dC). Biochimie. 1988 Feb;70(2):221–226. doi: 10.1016/0300-9084(88)90064-8. [DOI] [PubMed] [Google Scholar]
  30. Thomas T. J., Messner R. P. Structural specificity of polyamines in left-handed Z-DNA formation. Immunological and spectroscopic studies. J Mol Biol. 1988 May 20;201(2):463–467. doi: 10.1016/0022-2836(88)90155-6. [DOI] [PubMed] [Google Scholar]
  31. Tinoco I., Jr, Bustamante C., Maestre M. F. The optical activity of nucleic acids and their aggregates. Annu Rev Biophys Bioeng. 1980;9:107–141. doi: 10.1146/annurev.bb.09.060180.000543. [DOI] [PubMed] [Google Scholar]
  32. Wells R. D., Brennan R., Chapman K. A., Goodman T. C., Hart P. A., Hillen W., Kellogg D. R., Kilpatrick M. W., Klein R. D., Klysik J. Left-handed DNA helices, supercoiling, and the B-Z junction. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):77–84. doi: 10.1101/sqb.1983.047.01.010. [DOI] [PubMed] [Google Scholar]
  33. Widom J., Baldwin R. L. Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. J Mol Biol. 1980 Dec 25;144(4):431–453. doi: 10.1016/0022-2836(80)90330-7. [DOI] [PubMed] [Google Scholar]
  34. Widom J., Baldwin R. L. Monomolecular condensation of lambda-DNA induced by cobalt hexamine. Biopolymers. 1983 Jun;22(6):1595–1620. doi: 10.1002/bip.360220612. [DOI] [PubMed] [Google Scholar]
  35. Wilson R. W., Bloomfield V. A. Counterion-induced condesation of deoxyribonucleic acid. a light-scattering study. Biochemistry. 1979 May 29;18(11):2192–2196. doi: 10.1021/bi00578a009. [DOI] [PubMed] [Google Scholar]
  36. Zacharias W., Martin J. C., Wells R. D. Condensed form of (dG-dC)n X (dG-dC)n as an intermediate between the B- and Z-type conformations induced by sodium acetate. Biochemistry. 1983 May 10;22(10):2398–2405. doi: 10.1021/bi00279a015. [DOI] [PubMed] [Google Scholar]
  37. Zarling D. A., Arndt-Jovin D. J., Robert-Nicoud M., McIntosh L. P., Thomae R., Jovin T. M. Immunoglobulin recognition of synthetic and natural left-handed Z DNA conformations and sequences. J Mol Biol. 1984 Jul 5;176(3):369–415. doi: 10.1016/0022-2836(84)90495-9. [DOI] [PubMed] [Google Scholar]
  38. van de Sande J. H., Jovin T. M. Z* DNA, the left-handed helical form of poly[d(G-C)] in MgCl2-ethanol, is biologically active. EMBO J. 1982;1(1):115–120. doi: 10.1002/j.1460-2075.1982.tb01133.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. van de Sande J. H., McIntosh L. P., Jovin T. M. Mn2+ and other transition metals at low concentration induce the right-to-left helical transformation of poly[d(G-C)]. EMBO J. 1982;1(7):777–782. doi: 10.1002/j.1460-2075.1982.tb01247.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES