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. 1988 Apr 25;16(8):3269–3281. doi: 10.1093/nar/16.8.3269

Early melting of supercoiled DNA.

Lyubchenko YuL 1, L S Shlyakhtenko 1
PMCID: PMC336493  PMID: 3375056

Abstract

Denaturing gradient gel electrophoresis (formamide with urea) has been used to study the melting of supercoiled DNA. A linear gradient of denaturant concentration proportional to a 25 degrees C linear increase of temperature (Teff) from the left to the right edge of the gel was created perpendicular to DNA migration. The mobility of supercoiled DNA molecules was shown to drop to the level of relaxed molecules a long way (5-30 degrees C) before linear DNA began to melt. The further increase of Teff, including the melting range for linear molecules, caused no appreciable changes in the mobility of relaxed molecules. The transition curves are S-shaped for all the topoisomers, and an increase of superhelicity shifts the transition towards lower Teff values. The analysis of the results indicates that the observed relaxation of superhelical molecules is due to denatured region forming in them, their size increasing with the topoisomer number.

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Selected References

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

  1. Burke R. L., Bauer W. R. The early melting of closed duplex DNA: analysis by banding in buoyant neutral rubidium trichloroacetate. Nucleic Acids Res. 1980 Mar 11;8(5):1145–1165. doi: 10.1093/nar/8.5.1145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Fischer S. G., Lerman L. S. Separation of random fragments of DNA according to properties of their sequences. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4420–4424. doi: 10.1073/pnas.77.8.4420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Kozyavkin S. A., Naritsin D. B., Lyubchenko YuL The kinetics of DNA helix-coil subtransitions. J Biomol Struct Dyn. 1986 Feb;3(4):689–704. doi: 10.1080/07391102.1986.10508456. [DOI] [PubMed] [Google Scholar]
  4. Lee F. S., Bauer W. R. Temperature dependence of the gel electrophoretic mobility of superhelical DNA. Nucleic Acids Res. 1985 Mar 11;13(5):1665–1682. doi: 10.1093/nar/13.5.1665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Lerman L. S., Fischer S. G., Hurley I., Silverstein K., Lumelsky N. Sequence-determined DNA separations. Annu Rev Biophys Bioeng. 1984;13:399–423. doi: 10.1146/annurev.bb.13.060184.002151. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Lyamichev V. I., Mirkin S. M., Frank-Kamenetskii M. D. Structures of homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1986 Feb;3(4):667–669. doi: 10.1080/07391102.1986.10508454. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Lyubchenko Y. L., Frank-Kamenetskii M. D., Vologodskii A. V., Lazurkin Y. S., Gause G. G., Jr Fine structure of DNA melting curves. Biopolymers. 1976 Jun;15(6):1019–1036. doi: 10.1002/bip.1976.360150602. [DOI] [PubMed] [Google Scholar]
  10. Nishigaki K., Husimi Y., Tsubota M. Detection of differences in higher order structure between highly homologous single-stranded DNAs by low-temperature denaturant gradient gel electrophoresis. J Biochem. 1986 Mar;99(3):663–671. doi: 10.1093/oxfordjournals.jbchem.a135525. [DOI] [PubMed] [Google Scholar]
  11. Oka A., Nomura N., Morita M., Sugisaki H., Sugimoto K., Takanami M. Nucleotide sequence of small ColE1 derivatives: structure of the regions essential for autonomous replication and colicin E1 immunity. Mol Gen Genet. 1979 May 4;172(2):151–159. doi: 10.1007/BF00268276. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Peck L. J., Wang J. C. Energetics of B-to-Z transition in DNA. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6206–6210. doi: 10.1073/pnas.80.20.6206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Razlutskii I. V., Shlyakhtenko L. S., Lyubchenko YuL The effect of nucleotide substitution on DNA denaturation profiles. Nucleic Acids Res. 1987 Aug 25;15(16):6665–6676. doi: 10.1093/nar/15.16.6665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Stirdivant S. M., Kłysik J., Wells R. D. Energetic and structural inter-relationship between DNA supercoiling and the right- to left-handed Z helix transitions in recombinant plasmids. J Biol Chem. 1982 Sep 10;257(17):10159–10165. [PubMed] [Google Scholar]
  16. Sullivan K. M., Lilley D. M. A dominant influence of flanking sequences on a local structural transition in DNA. Cell. 1986 Dec 5;47(5):817–827. doi: 10.1016/0092-8674(86)90524-6. [DOI] [PubMed] [Google Scholar]
  17. Vologodskii A. V., Frank-Kamenetskii M. D. Premelting of superhelical DNA: an expression for superhelical energy. FEBS Lett. 1981 Aug 17;131(1):178–180. doi: 10.1016/0014-5793(81)80914-3. [DOI] [PubMed] [Google Scholar]
  18. Vologodskii A. V. Obrazovanie nekanonicheskikh struktur v sverkhspiral'noi DNK. Vzaimnoe vliianie razlichnykh perekhodov. Mol Biol (Mosk) 1985 May-Jun;19(3):687–692. [PubMed] [Google Scholar]

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