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. 1979 Aug 10;6(11):3519–3534. doi: 10.1093/nar/6.11.3519

Interactions of 4', 6-diamidine-2-phenylindole with synthetic polynucleotides.

J Kapuściński, W Szer
PMCID: PMC327953  PMID: 493113

Abstract

4', 6-Diamidine-2-phenylindole forms fluorescent complexes with synthetic DNA duplexes containing AT, AU and IC base pairs; no fluorescent complexes were observed with duplexes containing GC base pairs or with duplexes containing a single AT base pair sandwiched between GC pairs. The binding site size is one molecule of dye per 3 base pairs. The intrinsic binding constants are higher for alternating sequence duplexes than for the corresponding homopolymer pairs. With the exception of the four-stranded helical poly rI which exhibits considerable fluorescence enhancement upon binding of the ligand, none of the single- or multi- stranded polyribonucleotides and ribo-deoxyribonucleotide hybrid structures form fluorescent complexes with the dye. Poly rI is the only RNA which forms a DNA B-like structure (Arnott et al. (1974) Biochem. J. 141, 537). The B conformation of the helix and the absence of guanine appear to be the major determinants of the specificity of the fluorescent binding mode of the dye. Nonfluorescent interactions of the dye with polynucleotides are nonspecific; UV absorption and circular dichroic spectra demonstrate binding to synthetic single- and double-stranded DNA and RNA analogs, including those containing GC base pairs.

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Selected References

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

  1. Arnott S., Chandrasekaran R., Marttila C. M. Structures for polyinosinic acid and polyguanylic acid. Biochem J. 1974 Aug;141(2):537–543. doi: 10.1042/bj1410537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baguley B. C., Falkenhaug E. M. The interaction of ethidium with synthetic double-stranded polynucleotides at low ionic strength. Nucleic Acids Res. 1978 Jan;5(1):161–171. doi: 10.1093/nar/5.1.161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cassani G. R., Bollum F. J. Oligodeoxythymidylate: polydeoxyadenylate and oligodeoxyadenylate: polydeoxythymidylate interactions. Biochemistry. 1969 Oct;8(10):3928–3936. doi: 10.1021/bi00838a008. [DOI] [PubMed] [Google Scholar]
  4. Cech C. L., Tinoco I., Jr Circular dichroism calculations for polyinosinic acid in proposed multi-stranded geometries. Nucleic Acids Res. 1976 Feb;3(2):399–404. doi: 10.1093/nar/3.2.399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chamberlin M. J. Comparative properties of DNA, RNA, and hybrid homopolymer pairs. Fed Proc. 1965 Nov-Dec;24(6):1446–1457. [PubMed] [Google Scholar]
  6. Chandra P., Mildner B., Dann O., Metz A. Influence of 4'-6'-diamidino-2-phenylindole on the secondary structure and template activities of DNA and polydeoxynucleotides. Mol Cell Biochem. 1977 Dec 29;18(2-3):81–86. doi: 10.1007/BF00280272. [DOI] [PubMed] [Google Scholar]
  7. Gaugain B., Barbet J., Capelle N., Roques B. P., Le Pecq J. B. DNA Bifunctional intercalators. 2. Fluorescence properties and DNA binding interaction of an ethidium homodimer and an acridine ethidium heterodimer. Biochemistry. 1978 Nov 28;17(24):5078–5088. doi: 10.1021/bi00617a002. [DOI] [PubMed] [Google Scholar]
  8. Gukovskaia A. S., Sukhorukov B. I., Gukovskii I. Ia. O vliianii solevogo sostava sredy na stekhiometriiu i stabil'nost' kompleksov polinukleotid--monomer. Biofizika. 1975 Nov-Dec;20(6):1127–1128. [PubMed] [Google Scholar]
  9. Kania J., Fanning T. G. Use of a sequence-specific DNA-binding ligand to probe the environments of EcoRI restriction endonuclease cleavage sites. Eur J Biochem. 1976 Aug 16;67(2):367–371. doi: 10.1111/j.1432-1033.1976.tb10700.x. [DOI] [PubMed] [Google Scholar]
  10. Kapuściński J., Skoczylas B. Fluorescent complexes of DNA with DAPI 4',6-diamidine-2-phenyl indole.2HCl or DCI 4',6-dicarboxyamide-2-phenyl indole. Nucleic Acids Res. 1978 Oct;5(10):3775–3799. doi: 10.1093/nar/5.10.3775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kapuściński J., Skoczylas B. Simple and rapid fluorimetric method for DNA microassay. Anal Biochem. 1977 Nov;83(1):252–257. doi: 10.1016/0003-2697(77)90533-4. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Lin M. S., Alfi O. S., Donnell G. N. Differential fluorescence of sister chromatids with 4'-6-diamidino-2-phenylindole. Can J Genet Cytol. 1976 Sep;18(3):545–547. doi: 10.1139/g76-068. [DOI] [PubMed] [Google Scholar]
  14. Maurizot J. C., Boubault G., Hélène C. Interaction of aromatic residues of proteins with nucleic acids. Binding of oligopeptides to copolynucleotides of adenine and cytosine. Biochemistry. 1978 May 30;17(11):2096–2101. doi: 10.1021/bi00604a012. [DOI] [PubMed] [Google Scholar]
  15. McGhee J. D., von Hippel P. H. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 1974 Jun 25;86(2):469–489. doi: 10.1016/0022-2836(74)90031-x. [DOI] [PubMed] [Google Scholar]
  16. Michelson A. M., Massoulié J., Guschlbauer W. Synthetic polynucleotides. Prog Nucleic Acid Res Mol Biol. 1967;6:83–141. doi: 10.1016/s0079-6603(08)60525-5. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Rogers G. T., Ulbricht T. L., Szer W. Interaction of polyuridylic acid and spermine. Biochem Biophys Res Commun. 1967 May 5;27(3):372–377. doi: 10.1016/s0006-291x(67)80109-8. [DOI] [PubMed] [Google Scholar]
  19. Sobell H. M., Tsai C. C., Jain S. C., Gilbert S. G. Visualization of drug-nucleic acid interactions at atomic resolution. III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions. J Mol Biol. 1977 Aug 15;114(3):333–365. doi: 10.1016/0022-2836(77)90254-6. [DOI] [PubMed] [Google Scholar]
  20. Stöhr M., Eipel H., Goerttler K., Vogt-Schaden M. Extended application of flow microfluorometry by means of dual laser excitation. Histochemistry. 1977 Apr 4;51(4):305–313. doi: 10.1007/BF00494366. [DOI] [PubMed] [Google Scholar]
  21. Szer W. Ordered state of poly-uridylic acid above room temperature. J Mol Biol. 1966 Apr;16(2):585–587. doi: 10.1016/s0022-2836(66)80200-0. [DOI] [PubMed] [Google Scholar]
  22. Wells R. D., Larson J. E., Grant R. C., Shortle B. E., Cantor C. R. Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J Mol Biol. 1970 Dec 28;54(3):465–497. doi: 10.1016/0022-2836(70)90121-x. [DOI] [PubMed] [Google Scholar]
  23. Zimmerman S. B. Letter to the editor: The polyuridylic acid complex with polyamines: an x-ray fiber diffraction observation. J Mol Biol. 1976 Mar 15;101(4):563–565. doi: 10.1016/0022-2836(76)90245-x. [DOI] [PubMed] [Google Scholar]

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