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. 1977 May;4(5):1667–1680. doi: 10.1093/nar/4.5.1667

A strong ethidium binding site in the acceptor stem of most or all transfer RNAs.

B D Wells, C R Cantor
PMCID: PMC343780  PMID: 331262

Abstract

E. coli unfractionated tRNA and tRNA phe both contain a single strong ethidium binding site. Singlet-singlet energy transfer has been used to measure the distance between this site and dansyl hydrazine covalently attached to the 3' end of the tRNAs. The distance obtained is between 33 and 40 A for both samples. This is completely consistent with results from earlier NMR studies which placed the single, strong ethidium binding site of yeast tRNAphe between base pairs 6 and 7 on the aminoacyl stem. From the known tertiary structure of tRNAphe it is possible to rationalize the unusual affinity of this site and its likely existence in all tRNAs.

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Selected References

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

  1. Bauer W., Vinograd J. The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. J Mol Biol. 1968 Apr 14;33(1):141–171. doi: 10.1016/0022-2836(68)90286-6. [DOI] [PubMed] [Google Scholar]
  2. Bittman R. Studies of the binding of ethidium bromide to transfer ribonucleic acid: absorption, fluorescence, ultracentrifugation and kinetic investigations. J Mol Biol. 1969 Dec 14;46(2):251–268. doi: 10.1016/0022-2836(69)90420-3. [DOI] [PubMed] [Google Scholar]
  3. Bollen A., Herzog A., Favre A., Thibault J., Gros F. Fluorescence studies on the 30 S ribosome assembly process. FEBS Lett. 1970 Nov 9;11(1):49–54. doi: 10.1016/0014-5793(70)80489-6. [DOI] [PubMed] [Google Scholar]
  4. Burns V. W. Fluorescence decay time characteristics of the complex between ethidium bromide and nucleic acids. Arch Biochem Biophys. 1969 Sep;133(2):420–424. doi: 10.1016/0003-9861(69)90471-8. [DOI] [PubMed] [Google Scholar]
  5. Cole P. E., Yang S. K., Crothers D. M. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry. 1972 Nov 7;11(23):4358–4368. doi: 10.1021/bi00773a024. [DOI] [PubMed] [Google Scholar]
  6. Fuenteun J., Monier R., Garrett R., Le Bret M., Le Pecq J. B. Effect of 50 S subunit proteins L5, L18 and L25 on the fluorescence of 5 S RNA-bound ethidium bromide. J Mol Biol. 1975 Apr 25;93(4):535–541. doi: 10.1016/0022-2836(75)90245-4. [DOI] [PubMed] [Google Scholar]
  7. Jones C. R., Kearns D. R. Identification of a unique ethidium bromide binding site on yeast tRNAPhe by high resolution (300 MHz) nuclear magnetic resonance. Biochemistry. 1975 Jun 17;14(12):2660–2665. doi: 10.1021/bi00683a016. [DOI] [PubMed] [Google Scholar]
  8. Pongs O., Wrede P., Erdmann V. A. Binding of complementary oligonucleotides to amino-acylated tRNAPhe from yeast. Biochem Biophys Res Commun. 1976 Aug 23;71(4):1025–1033. doi: 10.1016/0006-291x(76)90757-9. [DOI] [PubMed] [Google Scholar]
  9. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 1976 Nov 19;194(4267):796–806. doi: 10.1126/science.790568. [DOI] [PubMed] [Google Scholar]
  10. Sobell H. M., Tsai C. C., Gilbert S. G., Jain S. C., Sakore T. D. Organization of DNA in chromatin. Proc Natl Acad Sci U S A. 1976 Sep;73(9):3068–3072. doi: 10.1073/pnas.73.9.3068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Sussman J. L., Kim S. Three-dimensional structure of a transfer rna in two crystal forms. Science. 1976 May 28;192(4242):853–858. doi: 10.1126/science.775636. [DOI] [PubMed] [Google Scholar]
  12. Tao T., Nelson J. H., Cantor C. R. Conformational studies on transfer ribonucleic acid. Fluorescence lifetime and nanosecond depolarization measurements on bound ethidium bromidee. Biochemistry. 1970 Sep 1;9(18):3514–3524. doi: 10.1021/bi00820a004. [DOI] [PubMed] [Google Scholar]
  13. Urbanke C., Römer R., Maass G. The binding of ethidium bromide to different conformations of tRNA. Unfolding of tertiary structure. Eur J Biochem. 1973 Mar 15;33(3):511–516. doi: 10.1111/j.1432-1033.1973.tb02710.x. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Waring M. J. Complex formation between ethidium bromide and nucleic acids. J Mol Biol. 1965 Aug;13(1):269–282. doi: 10.1016/s0022-2836(65)80096-1. [DOI] [PubMed] [Google Scholar]

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