Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1975 Feb;72(2):628–632. doi: 10.1073/pnas.72.2.628

X-ray crystallographic visualization of drug-nucleic acid intercalative binding: structure of an ethidium-dinucleoside monophosphate crystalline complex, Ethidium: 5-iodouridylyl (3'-5') adenosine.

C C Tsai, S C Jain, H M Sobell
PMCID: PMC432367  PMID: 1054844

Abstract

We have cocrystallized the drug ethidium bromide with the dinucleoside monophosphate 5-iodouridylyl(3'-5')adenosine and have solved the three-dimensional structure to atomic resolution by x-ray crystallography. This has allowed the direct visualization of intercalative binding by this drug to a fragment of a nucleic acid double helix.

Full text

PDF
629

Selected References

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

  1. Bauer W., Vinograd J. Interaction of closed circular DNA with intercalative dyes. II. The free energy of superhelix formation in SV40 DNA. J Mol Biol. 1970 Feb 14;47(3):419–435. doi: 10.1016/0022-2836(70)90312-8. [DOI] [PubMed] [Google Scholar]
  2. Crawford L. V., Waring M. J. Supercoiling of polyoma virus DNA measured by its interaction with ethidium bromide. J Mol Biol. 1967 Apr 14;25(1):23–30. doi: 10.1016/0022-2836(67)90276-8. [DOI] [PubMed] [Google Scholar]
  3. Dale R. M., Livingston D. C., Ward D. C. The synthesis and enzymatic polymerization of nucleotides containing mercury: potential tools for nucleic acid sequencing and structural analysis. Proc Natl Acad Sci U S A. 1973 Aug;70(8):2238–2242. doi: 10.1073/pnas.70.8.2238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Day R. O., Seeman N. C., Rosenberg J. M., Rich A. A crystalline fragment of the double helix: the structure of the dinucleoside phosphate guanylyl-3',5'-cytidine. Proc Natl Acad Sci U S A. 1973 Mar;70(3):849–853. doi: 10.1073/pnas.70.3.849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Freifelder D. Electron microscopic study of the ethidium bromide-DNA complex. J Mol Biol. 1971 Sep 14;60(2):401–403. doi: 10.1016/0022-2836(71)90303-2. [DOI] [PubMed] [Google Scholar]
  6. Hirota Y. THE EFFECT OF ACRIDINE DYES ON MATING TYPE FACTORS IN ESCHERICHIA COLI. Proc Natl Acad Sci U S A. 1960 Jan;46(1):57–64. doi: 10.1073/pnas.46.1.57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. LERMAN L. S. The structure of the DNA-acridine complex. Proc Natl Acad Sci U S A. 1963 Jan 15;49:94–102. doi: 10.1073/pnas.49.1.94. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Maniatis T., Ptashne M. Multiple repressor binding at the operators in bacteriophage lambda. Proc Natl Acad Sci U S A. 1973 May;70(5):1531–1535. doi: 10.1073/pnas.70.5.1531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Müller W., Crothers D. M. Studies of the binding of actinomycin and related compounds to DNA. J Mol Biol. 1968 Jul 28;35(2):251–290. doi: 10.1016/s0022-2836(68)80024-5. [DOI] [PubMed] [Google Scholar]
  12. NEWTON B. A. MECHANISMS OF ACTION OF PHENANTHRIDINE AND AMINOQUINALDINE TRYPANOCIDES. Adv Chemother. 1964;25:35–83. doi: 10.1016/b978-1-4831-9929-0.50008-5. [DOI] [PubMed] [Google Scholar]
  13. O'Brien R. L., Allison J. L., Hahn F. E. Evidence for intercalation of chloroquine into DNA. Biochim Biophys Acta. 1966 Dec 21;129(3):622–624. doi: 10.1016/0005-2787(66)90078-5. [DOI] [PubMed] [Google Scholar]
  14. Pigram W. J., Fuller W., Hamilton L. D. Stereochemistry of intercalation: interaction of daunomycin with DNA. Nat New Biol. 1972 Jan 5;235(53):17–19. doi: 10.1038/newbio235017a0. [DOI] [PubMed] [Google Scholar]
  15. Rosenberg J. M., Seeman N. C., Kim J. J., Suddath F. L., Nicholas H. B., Rich A. Double helix at atomic resolution. Nature. 1973 May 18;243(5403):150–154. doi: 10.1038/243150a0. [DOI] [PubMed] [Google Scholar]
  16. Saucier J. M., Wang J. C. Angular alteration of the DNA helix by E. coli RNA polymerase. Nat New Biol. 1972 Oct 11;239(93):167–170. doi: 10.1038/newbio239167a0. [DOI] [PubMed] [Google Scholar]
  17. Sobell H. M., Jain S. C. Stereochemistry of actinomycin binding to DNA. II. Detailed molecular model of actinomycin-DNA complex and its implications. J Mol Biol. 1972 Jul 14;68(1):21–34. doi: 10.1016/0022-2836(72)90259-8. [DOI] [PubMed] [Google Scholar]
  18. WARING M. J. COMPLEX FORMATION WITH DNA AND INHIBITION OF ESCHERICHIA COLI RNA POLYMERASE BY ETHIDIUM BROMIDE. Biochim Biophys Acta. 1964 Jun 22;87:358–361. doi: 10.1016/0926-6550(64)90238-5. [DOI] [PubMed] [Google Scholar]
  19. Wang J. C. The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J Mol Biol. 1974 Nov 15;89(4):783–801. doi: 10.1016/0022-2836(74)90053-9. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Waring M. Variation of the supercoils in closed circular DNA by binding of antibiotics and drugs: evidence for molecular models involving intercalation. J Mol Biol. 1970 Dec 14;54(2):247–279. doi: 10.1016/0022-2836(70)90429-8. [DOI] [PubMed] [Google Scholar]
  22. Wells R. D., Larson J. E. Studies on the binding of actinomycin D to DNA and DNA model polymers. J Mol Biol. 1970 Apr 28;49(2):319–342. doi: 10.1016/0022-2836(70)90248-2. [DOI] [PubMed] [Google Scholar]
  23. Zylber E., Vesco C., Penman S. Selective inhibition of the synthesis of mitochondria-associated RNA by ethidium bromide. J Mol Biol. 1969 Aug 28;44(1):195–204. doi: 10.1016/0022-2836(69)90414-8. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES