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. 1983 Nov 11;11(21):7555–7568. doi: 10.1093/nar/11.21.7555

Increased accessibility of bases in DNA upon binding of acridine orange.

J Kapuscinski, Z Darzynkiewicz
PMCID: PMC326502  PMID: 6647029

Abstract

Acridine orange (AO) forms 1:1 complexes with dsDNA which are insoluble in aqueous media, exhibit red luminescence, have minimal green luminescence and resemble complexes of AO with ss nucleic acids. During formation and/or dissociation of these complexes, accessibility of DNA bases to two conformational probes, formaldehyde and diethyl pyrocarbonate is increased, suggesting that the base pairing is destroyed and DNA at least partially denatured. Adriamycin and Ellipticine, but not Ethidium Bromide exert similar destabilizing effects. The results confirm our earlier predictions based on thermodynamic calculations that the double helix undergoes destabilization upon binding an intercalator characterized by high cooperativity in interaction with ss nucleic acids. Thus, the highly cooperative ligand binding to ss sections during the "breathing" of the polymer may progressively destabilize the adjacent ds structure.

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Selected References

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  1. Armstrong R. W., Kurucsev T., Strauss U. P. The interaction between acridine dyes and deoxyribonucleic acid. J Am Chem Soc. 1970 May 20;92(10):3174–3181. doi: 10.1021/ja00713a041. [DOI] [PubMed] [Google Scholar]
  2. Blake A., Peacocke A. R. The interaction of aminocridines with nucleic acids. Biopolymers. 1968;6(9):1225–1253. doi: 10.1002/bip.1968.360060902. [DOI] [PubMed] [Google Scholar]
  3. Bradley D. F., Wolf M. K. AGGREGATION OF DYES BOUND TO POLYANIONS. Proc Natl Acad Sci U S A. 1959 Jul;45(7):944–952. doi: 10.1073/pnas.45.7.944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Darzynkiewicz Z., Traganos F., Sharpless T., Melamed M. R. Conformation of RNA in situ as studied by acridine orange staining and automated cytofluorometry. Exp Cell Res. 1975 Oct 1;95(1):143–153. doi: 10.1016/0014-4827(75)90619-9. [DOI] [PubMed] [Google Scholar]
  5. Darzynkiewicz Z., Traganos F., Sharpless T., Melamed M. Thermally-induced changes in chromatin of isolated nuclei and of intact cells as revealed by acridine orange staining. Biochem Biophys Res Commun. 1974 Jul 10;59(1):392–399. doi: 10.1016/s0006-291x(74)80219-6. [DOI] [PubMed] [Google Scholar]
  6. Darzynkiewicz Z., Tragnos F., Sharpless T., Friend C., Melamed M. R. Nuclear chromatin changes during erythroid differentiation of friend virus induced leukemic cells. Exp Cell Res. 1976 May;99(2):301–309. doi: 10.1016/0014-4827(76)90587-5. [DOI] [PubMed] [Google Scholar]
  7. Ehrenberg L., Fedorcsak I., Solymosy F. Diethyl pyrocarbonate in nucleic acid research. Prog Nucleic Acid Res Mol Biol. 1976;16:189–262. doi: 10.1016/s0079-6603(08)60758-8. [DOI] [PubMed] [Google Scholar]
  8. Felsenfeld G., Hirschman S. Z. A neighbor-interaction analysis of the hypochromism and spectra of DNA. J Mol Biol. 1965 Sep;13(2):407–427. doi: 10.1016/s0022-2836(65)80106-1. [DOI] [PubMed] [Google Scholar]
  9. IYER V. N., SZYBALSKI W. A MOLECULAR MECHANISM OF MITOMYCIN ACTION: LINKING OF COMPLEMENTARY DNA STRANDS. Proc Natl Acad Sci U S A. 1963 Aug;50:355–362. doi: 10.1073/pnas.50.2.355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ichimura S., Zama M., Fujita H., Ito T. The nature of strong binding between acridine orange and deoxyribonucleic acid as revealed by equilibrium dialysis and thermal renaturation. Biochim Biophys Acta. 1969 Sep 17;190(1):116–125. doi: 10.1016/0005-2787(69)90160-9. [DOI] [PubMed] [Google Scholar]
  11. Ichimura S., Zama M., Fujita H. Quantitative determination of single-stranded sections in DNA using the fluorescent probe acridine orange. Biochim Biophys Acta. 1971 Jul 29;240(4):485–495. doi: 10.1016/0005-2787(71)90705-2. [DOI] [PubMed] [Google Scholar]
  12. KLEINWAECHTER V., KOUDELKA J. THERMAL DENATURATION OF DEOXYRIBONUCLEIC ACID-ACRIDINE ORANGE COMPLEXES. Biochim Biophys Acta. 1964 Nov 15;91:539–540. doi: 10.1016/0926-6550(64)90088-x. [DOI] [PubMed] [Google Scholar]
  13. Kapuscinski J., Darzynkiewicz Z., Melamed M. R. Luminescence of the solid complexes of acridine orange with RNA. Cytometry. 1982 Jan;2(4):201–211. doi: 10.1002/cyto.990020402. [DOI] [PubMed] [Google Scholar]
  14. Kapuscinski J., Darzynkiewicz Z., Traganos F., Melamed M. R. Interactions of a new antitumor agent, 1,4-dihydroxy-5,8-bis[[2-[(2-hydroxyethyl)amino]-ethyl]amino]-9,10-anthracenedione, with nucleic acids. Biochem Pharmacol. 1981 Feb 1;30(3):231–240. doi: 10.1016/0006-2952(81)90083-6. [DOI] [PubMed] [Google Scholar]
  15. Kelly R. C., Jensen D. E., von Hippel P. H. DNA "melting" proteins. IV. Fluorescence measurements of binding parameters for bacteriophage T4 gene 32-protein to mono-, oligo-, and polynucleotides. J Biol Chem. 1976 Nov 25;251(22):7240–7250. [PubMed] [Google Scholar]
  16. Kohn K. W., Waring M. J., Glaubiger D., Friedman C. A. Intercalative binding of ellipticine to DNA. Cancer Res. 1975 Jan;35(1):71–76. [PubMed] [Google Scholar]
  17. LERMAN L. S. Structural considerations in the interaction of DNA and acridines. J Mol Biol. 1961 Feb;3:18–30. doi: 10.1016/s0022-2836(61)80004-1. [DOI] [PubMed] [Google Scholar]
  18. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978 May;11(2):179–246. doi: 10.1017/s0033583500002031. [DOI] [PubMed] [Google Scholar]
  19. McGhee J. D. Theoretical calculations of the helix-coil transition of DNA in the presence of large, cooperatively binding ligands. Biopolymers. 1976 Jul;15(7):1345–1375. doi: 10.1002/bip.1976.360150710. [DOI] [PubMed] [Google Scholar]
  20. McGhee J. D., von Hippel P. H. Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry. 1975 Mar 25;14(6):1281–1296. doi: 10.1021/bi00677a029. [DOI] [PubMed] [Google Scholar]
  21. Miller K. J., Pycior J. F. Interaction of molecules with nucleic acids. II. Two pairs of families of intercalation sites, unwinding angles, and the neighbor-exclusion principle. Biopolymers. 1979 Nov;18(11):2683–2719. doi: 10.1002/bip.1979.360181105. [DOI] [PubMed] [Google Scholar]
  22. Neville D. M., Jr, Davies D. R. The interaction of acridine dyes with DNA: an x-ray diffraction and optical investigation. J Mol Biol. 1966 May;17(1):57–74. doi: 10.1016/s0022-2836(66)80094-3. [DOI] [PubMed] [Google Scholar]
  23. Oberg B. Carbethoxylation of polynucleotides. Eur J Biochem. 1971 Apr 30;19(4):496–501. doi: 10.1111/j.1432-1033.1971.tb01340.x. [DOI] [PubMed] [Google Scholar]
  24. Porumb H. The solution spectroscopy of drugs and the drug-nucleic acid interactions. Prog Biophys Mol Biol. 1978;34(3):175–195. doi: 10.1016/0079-6107(79)90017-8. [DOI] [PubMed] [Google Scholar]
  25. Record M. T., Jr, Mazur S. J., Melançon P., Roe J. H., Shaner S. L., Unger L. Double helical DNA: conformations, physical properties, and interactions with ligands. Annu Rev Biochem. 1981;50:997–1024. doi: 10.1146/annurev.bi.50.070181.005025. [DOI] [PubMed] [Google Scholar]
  26. Saucier J. M. Physicochemical studies on the interaction of irehdiamine A with bihelical DNA. Biochemistry. 1977 Dec 27;16(26):5879–5889. doi: 10.1021/bi00645a036. [DOI] [PubMed] [Google Scholar]
  27. Scott J. E. On the mechanism of the methyl green-pyronin stain for nucleic acids. Histochemie. 1967;9(1):30–47. doi: 10.1007/BF00281805. [DOI] [PubMed] [Google Scholar]
  28. Toulmé J. J., Hélène C. Specific recognition of single-stranded nucleic acids. Interaction of tryptophan-containing peptides with native, denatured, and ultraviolet-irradiated DNA. J Biol Chem. 1977 Jan 10;252(1):244–249. [PubMed] [Google Scholar]
  29. Wakelin L. P., Adams A., Hunter C., Waring M. J. Interaction of crystal violet with nucleic acids. Biochemistry. 1981 Sep 29;20(20):5779–5787. doi: 10.1021/bi00523a021. [DOI] [PubMed] [Google Scholar]
  30. Waring M. J. DNA modification and cancer. Annu Rev Biochem. 1981;50:159–192. doi: 10.1146/annurev.bi.50.070181.001111. [DOI] [PubMed] [Google Scholar]
  31. Waring M. J. Structural requirements for the binding of ethidium to nucleic acids. Biochim Biophys Acta. 1966 Feb 21;114(2):234–244. doi: 10.1016/0005-2787(66)90305-4. [DOI] [PubMed] [Google Scholar]
  32. Widom J., Baldwin R. L. Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. J Mol Biol. 1980 Dec 25;144(4):431–453. doi: 10.1016/0022-2836(80)90330-7. [DOI] [PubMed] [Google Scholar]
  33. Yguerabide J. Nanosecond fluorescence spectroscopy of macromolecules. Methods Enzymol. 1972;26:498–578. doi: 10.1016/s0076-6879(72)26026-8. [DOI] [PubMed] [Google Scholar]
  34. Zunino F., Gambetta R., Di Marco A., Zaccara A. Interaction of daunomycin and its derivatives with DNA. Biochim Biophys Acta. 1972 Sep 14;277(3):489–498. doi: 10.1016/0005-2787(72)90092-5. [DOI] [PubMed] [Google Scholar]
  35. von Tscharner V., Schwarz G. Complex formation of acridine orange with single-stranded polyriboadenylic acid and 5'-AMP: cooperative binding and intercalation between bases. Biophys Struct Mech. 1979 Mar 21;5(1):75–90. doi: 10.1007/BF00535774. [DOI] [PubMed] [Google Scholar]

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