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. 1982 Jun;79(11):3518–3522. doi: 10.1073/pnas.79.11.3518

Molecular motion of DNA as measured by triplet anisotropy decay.

M Hogan, J Wang, R H Austin, C L Monitto, S Hershkowitz
PMCID: PMC346452  PMID: 6954497

Abstract

We have used triplet anisotropy decay techniques to measure the internal flexibility and overall rotational motion of DNA, covering a time range from 15 ns to 200 mus. Nearly monodisperse DNA fragments 65--600 base pairs long were studied by using the intercalating dye methylene blue as a triplet probe. We found that the slow end-over-end tumbling of short DNA fragments (less than or equal to 165 base pairs) is as predicted for a rigid rod. As expected, a longer DNA fragment (600 base pairs) experiences slow segmental motion of its helix axis. We found that, at the earliest times, anisotropy decays more rapidly than expected for a rigid rod, suggesting that, when bound, methylene blue monitors fast internal motion of the helix. Since the rod-like end-over-end tumbling of short fragments rules out fast bending motions, we conclude that the fast components of DNA anisotropy decay are due to twisting motion of the helix, occurring with a time constant near 50 ns.

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Selected References

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

  1. Austin R. H., Chan S. S., Jovin T. M. Rotational diffusion of cell surface components by time-resolved phosphorescence anisotropy. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5650–5654. doi: 10.1073/pnas.76.11.5650. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Belford G. G., Belford R. L., Weber G. Dynamics of fluorescence polarization in macromolecules. Proc Natl Acad Sci U S A. 1972 Jun;69(6):1392–1393. doi: 10.1073/pnas.69.6.1392. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Hogan M. E., Jardetzky O. Effect of ethidium bromide on deoxyribonucleic acid internal motions. Biochemistry. 1980 May 13;19(10):2079–2085. doi: 10.1021/bi00551a012. [DOI] [PubMed] [Google Scholar]
  4. Hogan M. E., Jardetzky O. Internal motions in DNA. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6341–6345. doi: 10.1073/pnas.76.12.6341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hogan M., Dattagupta N., Crothers D. M. Transient electric dichroism of rod-like DNA molecules. Proc Natl Acad Sci U S A. 1978 Jan;75(1):195–199. doi: 10.1073/pnas.75.1.195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hogan M., Dattagupta N., Crothers D. M. Transient electric dichroism studies of the structure of the DNA complex with intercalated drugs. Biochemistry. 1979 Jan 23;18(2):280–288. doi: 10.1021/bi00569a007. [DOI] [PubMed] [Google Scholar]
  7. Jolly D., Eisenberg H. Photon correlation spectroscopy, total intensity light scattering with laser radiation, and hydrodynamic studies of a well fractionated DNA sample. Biopolymers. 1976 Jan;15(1):61–95. doi: 10.1002/bip.1976.360150107. [DOI] [PubMed] [Google Scholar]
  8. Jovin T. M., Bartholdi M., Vaz W. L., Austin R. H. Rotational diffusion of biological macromolecules by time-resolved delayed luminescence (phosphorescence, fluorescence) anisotropy. Ann N Y Acad Sci. 1981;366:176–196. doi: 10.1111/j.1749-6632.1981.tb20753.x. [DOI] [PubMed] [Google Scholar]
  9. Klevan L., Armitage I. M., Crothers D. M. 31P NMR studies of the solution structure and dynamics of nucleosomes and DNA. Nucleic Acids Res. 1979 Apr;6(4):1607–1616. doi: 10.1093/nar/6.4.1607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. LePecq J. B., Paoletti C. A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization. J Mol Biol. 1967 Jul 14;27(1):87–106. doi: 10.1016/0022-2836(67)90353-1. [DOI] [PubMed] [Google Scholar]
  11. Lipari G., Szabo A. Effect of librational motion on fluorescence depolarization and nuclear magnetic resonance relaxation in macromolecules and membranes. Biophys J. 1980 Jun;30(3):489–506. doi: 10.1016/S0006-3495(80)85109-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Millar D. P., Robbins R. J., Zewail A. H. Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. Proc Natl Acad Sci U S A. 1980 Oct;77(10):5593–5597. doi: 10.1073/pnas.77.10.5593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Robinson B. H., Lerman L. S., Beth A. H., Frisch H. L., Dalton L. R., Auer C. Analysis of double-helix motions with spin-labeled probes: binding geometry and the limit of torsional elasticity. J Mol Biol. 1980 May 5;139(1):19–44. doi: 10.1016/0022-2836(80)90113-8. [DOI] [PubMed] [Google Scholar]
  14. Thomas J. C., Allison S. A., Appellof C. J., Schurr J. M. Torison dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral phi 29 DNA. Biophys Chem. 1980 Oct;12(2):177–188. doi: 10.1016/0301-4622(80)80050-0. [DOI] [PubMed] [Google Scholar]
  15. Wahl P., Paoletti J., Le Pecq J. B. Decay of fluorescence emission anisotropy of the ethidium bromide-DNA complex. Evidence for an internal motion in DNA. Proc Natl Acad Sci U S A. 1970 Feb;65(2):417–421. doi: 10.1073/pnas.65.2.417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Waring M. J., Wakelin L. P., Lee J. S. A solvent-partition method for measuring the binding of drugs to DNA. Application to the quinoxaline antibiotics echinomycin and triostin A. Biochim Biophys Acta. 1975 Oct 1;407(2):200–212. doi: 10.1016/0005-2787(75)90285-3. [DOI] [PubMed] [Google Scholar]
  17. Wing R., Drew H., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Crystal structure analysis of a complete turn of B-DNA. Nature. 1980 Oct 23;287(5784):755–758. doi: 10.1038/287755a0. [DOI] [PubMed] [Google Scholar]

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