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. 1998 Mar 15;26(6):1503–1508. doi: 10.1093/nar/26.6.1503

Non-complementary DNA helical structure induced by positive torsional stress.

A V Vologodskii 1, X Yang 1, N C Seeman 1
PMCID: PMC147419  PMID: 9490798

Abstract

We have induced a local conformational transition by positive torsional stress in small synthetic circular DNA molecules containing cruciforms with immobile or tetramobile branched junctions. The immobile species correspond to the extruded and intruded extrema of the tetramobile junction. Under normal conditions the sequences of all the branched species prevent them from being re-absorbed into the circle. We have induced positive stress by addition of ethidium to the circle, in a low ionic strength medium. Alterations in gel electrophoretic mobility under increasing concentrations of ethidium suggest that the cruciforms undergo a transition under torsional stress. The product of this transition contains mispaired nucleotides, but interwound backbones. By comparing the electrophoretic mobilities of circles containing these structures with that of a completely complementary circle of the same length, we conclude that the twist in the mispairing region is similiar to that of completely paired species.

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Selected References

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  1. Bauer W., Vinograd J. Interaction of closed circular DNA with intercalative dyes. II. The free energy of superhelix formation in SV40 DNA. J Mol Biol. 1970 Feb 14;47(3):419–435. doi: 10.1016/0022-2836(70)90312-8. [DOI] [PubMed] [Google Scholar]
  2. Berman H. M., Olson W. K., Beveridge D. L., Westbrook J., Gelbin A., Demeny T., Hsieh S. H., Srinivasan A. R., Schneider B. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992 Sep;63(3):751–759. doi: 10.1016/S0006-3495(92)81649-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Caruthers M. H. Gene synthesis machines: DNA chemistry and its uses. Science. 1985 Oct 18;230(4723):281–285. doi: 10.1126/science.3863253. [DOI] [PubMed] [Google Scholar]
  4. Chaires J. B. Dissecting the free energy of drug binding to DNA. Anticancer Drug Des. 1996 Dec;11(8):569–580. [PubMed] [Google Scholar]
  5. Courey A. J., Wang J. C. Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions. Cell. 1983 Jul;33(3):817–829. doi: 10.1016/0092-8674(83)90024-7. [DOI] [PubMed] [Google Scholar]
  6. Courey A. J., Wang J. C. Influence of DNA sequence and supercoiling on the process of cruciform formation. J Mol Biol. 1988 Jul 5;202(1):35–43. doi: 10.1016/0022-2836(88)90516-5. [DOI] [PubMed] [Google Scholar]
  7. Gellert M., Mizuuchi K., O'Dea M. H., Ohmori H., Tomizawa J. DNA gyrase and DNA supercoiling. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):35–40. doi: 10.1101/sqb.1979.043.01.007. [DOI] [PubMed] [Google Scholar]
  8. Gellert M., O'Dea M. H., Mizuuchi K. Slow cruciform transitions in palindromic DNA. Proc Natl Acad Sci U S A. 1983 Sep;80(18):5545–5549. doi: 10.1073/pnas.80.18.5545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Horowitz D. S., Wang J. C. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol. 1984 Feb 15;173(1):75–91. doi: 10.1016/0022-2836(84)90404-2. [DOI] [PubMed] [Google Scholar]
  10. Johnston B. H. Generation and detection of Z-DNA. Methods Enzymol. 1992;211:127–158. doi: 10.1016/0076-6879(92)11009-8. [DOI] [PubMed] [Google Scholar]
  11. Lilley D. M. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468–6472. doi: 10.1073/pnas.77.11.6468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lyamichev V. I., Panyutin I. G., Frank-Kamenetskii M. D. Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis. FEBS Lett. 1983 Mar 21;153(2):298–302. doi: 10.1016/0014-5793(83)80628-0. [DOI] [PubMed] [Google Scholar]
  13. Murchie A. I., Lilley D. M. Supercoiled DNA and cruciform structures. Methods Enzymol. 1992;211:158–180. doi: 10.1016/0076-6879(92)11010-g. [DOI] [PubMed] [Google Scholar]
  14. Otokiti E. O., Sheardy R. D. Effect of base pair A/C and G/T mismatches on the thermal stabilities of DNA oligomers that form B-Z junctions. Biochemistry. 1997 Sep 23;36(38):11419–11427. doi: 10.1021/bi970972s. [DOI] [PubMed] [Google Scholar]
  15. Panayotatos N., Wells R. D. Cruciform structures in supercoiled DNA. Nature. 1981 Feb 5;289(5797):466–470. doi: 10.1038/289466a0. [DOI] [PubMed] [Google Scholar]
  16. Panyutin I., Klishko V., Lyamichev V. Kinetics of cruciform formation and stability of cruciform structure in superhelical DNA. J Biomol Struct Dyn. 1984 Jun;1(6):1311–1324. doi: 10.1080/07391102.1984.10507522. [DOI] [PubMed] [Google Scholar]
  17. Pohl F. M. Salt-induced transition between two double-helical forms of oligo (dC-dG). Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):113–117. doi: 10.1101/sqb.1983.047.01.014. [DOI] [PubMed] [Google Scholar]
  18. Rich A., Nordheim A., Wang A. H. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791–846. doi: 10.1146/annurev.bi.53.070184.004043. [DOI] [PubMed] [Google Scholar]
  19. Rybenkov V. V., Cozzarelli N. R., Vologodskii A. V. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5307–5311. doi: 10.1073/pnas.90.11.5307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Seeman N. C. Nucleic acid junctions and lattices. J Theor Biol. 1982 Nov 21;99(2):237–247. doi: 10.1016/0022-5193(82)90002-9. [DOI] [PubMed] [Google Scholar]
  21. Shore D., Baldwin R. L. Energetics of DNA twisting. II. Topoisomer analysis. J Mol Biol. 1983 Nov 15;170(4):983–1007. doi: 10.1016/s0022-2836(83)80199-5. [DOI] [PubMed] [Google Scholar]
  22. Sinden R. R., Pettijohn D. E. Cruciform transitions in DNA. J Biol Chem. 1984 May 25;259(10):6593–6600. [PubMed] [Google Scholar]
  23. Wang J. C. Helical repeat of DNA in solution. Proc Natl Acad Sci U S A. 1979 Jan;76(1):200–203. doi: 10.1073/pnas.76.1.200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Wang J. C. The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J Mol Biol. 1974 Nov 15;89(4):783–801. doi: 10.1016/0022-2836(74)90053-9. [DOI] [PubMed] [Google Scholar]
  25. Wells R. D. Unusual DNA structures. J Biol Chem. 1988 Jan 25;263(3):1095–1098. [PubMed] [Google Scholar]
  26. Wilson W. D., Krishnamoorthy C. R., Wang Y. H., Smith J. C. Mechanism of intercalation: ion effects on the equilibrium and kinetic constants for the interaction of propidium and ethidium with DNA. Biopolymers. 1985 Oct;24(10):1941–1961. doi: 10.1002/bip.360241008. [DOI] [PubMed] [Google Scholar]
  27. Yang X., Vologodskii A. V., Liu B., Kemper B., Seeman N. C. Torsional control of double-stranded DNA branch migration. Biopolymers. 1998;45(1):69–83. doi: 10.1002/(SICI)1097-0282(199801)45:1<69::AID-BIP6>3.0.CO;2-X. [DOI] [PubMed] [Google Scholar]

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