Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Mar 11;15(5):2175–2189. doi: 10.1093/nar/15.5.2175

A tentative model of the intercalative binding of the neocarzinostatin chromophore to double-stranded tetranucleotides.

K X Chen, N Gresh, B Pullman
PMCID: PMC340625  PMID: 2951653

Abstract

Theoretical computations are performed of the intercalative binding of the neocarzinostatin chromophore (NCS) with the double-stranded oligonucleotides d(CGCG)2, d(GCGC)2, d(TATA)2 and d(ATAT)2. Minor groove binding is preferred over major groove binding. It is found that the long axis of the stacked naphtoate ring lies approximately parallel to the long axis of the base pairs of the intercalation site. The galactosamine ammonium group interacts with specific sites of the groove (O2/N3 of bases 2 and O1' of sugar S3), whereas the dodecadyine ring system wraps around the groove towards the backbone. An overall AT versus GC preference is derived. Intercalation in a central purine-(3', 5')-pyrimidine sequence appears to be preferred over that in a central pyrimidine-(3', 5')-purine sequence.

Full text

PDF
2175

Images in this article

2182Image
on p.2182

Selected References

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

  1. Arnott S., Hukins D. W. Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J Mol Biol. 1973 Dec 5;81(2):93–105. doi: 10.1016/0022-2836(73)90182-4. [DOI] [PubMed] [Google Scholar]
  2. Chen K. S., Gresh N., Pullman B. A theoretical investigation on the sequence selective binding of adriamycin to double-stranded polynucleotides. Nucleic Acids Res. 1986 Mar 11;14(5):2251–2267. doi: 10.1093/nar/14.5.2251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen K. X., Gresh N., Pullman B. A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides. J Biomol Struct Dyn. 1985 Dec;3(3):445–466. doi: 10.1080/07391102.1985.10508434. [DOI] [PubMed] [Google Scholar]
  4. Chen K. X., Gresh N., Pullman B. A theoretical investigation on the sequence selective binding of mitoxantrone to double-stranded tetranucleotides. Nucleic Acids Res. 1986 May 12;14(9):3799–3812. doi: 10.1093/nar/14.9.3799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen K. X., Gresh N., Pullman B. A theoretical study of anthracene and phenanthrene derivatives acting as A-T specific intercalators. Nucleic Acids Res. 1986 Nov 25;14(22):9103–9115. doi: 10.1093/nar/14.22.9103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chen K. X., Gresh N., Pullman B. A theoretical study of the comparative binding affinities of daunomycin derivatives to a double-stranded oligomeric DNA. Proposal for new high affinity derivatives. Mol Pharmacol. 1986 Sep;30(3):279–286. [PubMed] [Google Scholar]
  7. Dasgupta D., Goldberg I. H. Mode of reversible binding of neocarzinostatin chromophore to DNA: base sequence dependency of binding. Nucleic Acids Res. 1986 Jan 24;14(2):1089–1105. doi: 10.1093/nar/14.2.1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dasgupta D., Goldberg I. H. Mode of reversible binding of neocarzinostatin chromophore to DNA: evidence for binding via the minor groove. Biochemistry. 1985 Nov 19;24(24):6913–6920. doi: 10.1021/bi00345a025. [DOI] [PubMed] [Google Scholar]
  9. Hensens O. D., Dewey R. S., Liesch J. M., Napier M. A., Reamer R. A., Smith J. L., Albers-Schönberg G., Goldberg I. H. Neocarzinostatin chromophore: presence of a highly strained ether ring and its reaction with mercaptan and sodium borohydride. Biochem Biophys Res Commun. 1983 Jun 15;113(2):538–547. doi: 10.1016/0006-291x(83)91759-x. [DOI] [PubMed] [Google Scholar]
  10. Kappen L. S., Goldberg I. H. Activation of neocarzinostatin chromophore and formation of nascent DNA damage do not require molecular oxygen. Nucleic Acids Res. 1985 Mar 11;13(5):1637–1648. doi: 10.1093/nar/13.5.1637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kappen L. S., Goldberg I. H. Deoxyribonucleic acid damage by neocarzinostatin chromophore: strand breaks generated by selective oxidation of C-5' of deoxyribose. Biochemistry. 1983 Oct 11;22(21):4872–4878. doi: 10.1021/bi00290a002. [DOI] [PubMed] [Google Scholar]
  12. Kappen L. S., Goldberg I. H., Liesch J. M. Identification of thymidine-5'-aldehyde at DNA strand breaks induced by neocarzinostatin chromophore. Proc Natl Acad Sci U S A. 1982 Feb;79(3):744–748. doi: 10.1073/pnas.79.3.744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Meienhofer J., Maeda H., Glaser C. B., Czombos J., Kuromizu K. Primary structure of neocarzinostatin, an antitumor protein. Science. 1972 Nov 24;178(4063):875–876. doi: 10.1126/science.178.4063.875. [DOI] [PubMed] [Google Scholar]
  14. Miller K. J. Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix. Biopolymers. 1979 Apr;18(4):959–980. doi: 10.1002/bip.1979.360180415. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Napier M. A., Goldberg I. H. Neocarzinostatin chromophore. Assignment of spectral properties and structural requirements for binding to DNA. Mol Pharmacol. 1983 Mar;23(2):500–510. [PubMed] [Google Scholar]
  17. Napier M. A., Holmquist B., Strydom D. J., Goldberg I. H. Neocarzinostatin: spectral characterization and separation of a non-protein chromophore. Biochem Biophys Res Commun. 1979 Jul 27;89(2):635–642. doi: 10.1016/0006-291x(79)90677-6. [DOI] [PubMed] [Google Scholar]
  18. Ornstein R. L., Rein R. Energetics of intercalation specificity. I. Backbone unwinding. Biopolymers. 1979 May;18(5):1277–1291. doi: 10.1002/bip.1979.360180517. [DOI] [PubMed] [Google Scholar]
  19. Povirk L. F., Dattagupta N., Warf B. C., Goldberg I. H. Neocarzinostatin chromophore binds to deoxyribonucleic acid by intercalation. Biochemistry. 1981 Jul 7;20(14):4007–4014. doi: 10.1021/bi00517a009. [DOI] [PubMed] [Google Scholar]
  20. Povirk L. F., Goldberg I. H. Competition between anaerobic covalent linkage of neocarzinostatin chromophore to deoxyribose in DNA and oxygen-dependent strand breakage and base release. Biochemistry. 1984 Dec 18;23(26):6304–6311. doi: 10.1021/bi00321a003. [DOI] [PubMed] [Google Scholar]
  21. Povirk L. F., Goldberg I. H. Covalent adducts of DNA and the nonprotein chromophore of neocarzinostatin contain a modified deoxyribose. Proc Natl Acad Sci U S A. 1982 Jan;79(2):369–373. doi: 10.1073/pnas.79.2.369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Povirk L. F., Goldberg I. H. Detection of neocarzinostatin chromophore-deoxyribose adducts as exonuclease-resistant sites in defined-sequence DNA. Biochemistry. 1985 Jul 16;24(15):4035–4040. doi: 10.1021/bi00336a035. [DOI] [PubMed] [Google Scholar]
  23. Pullman A., Pullman B. Molecular electrostatic potential of the nucleic acids. Q Rev Biophys. 1981 Aug;14(3):289–380. doi: 10.1017/s0033583500002341. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Suzuki H., Miura K., Kumada Y., Takeuchi T., Tanaka N. Biological activities of non-protein chromophores of antitumor protein antibiotics: auromycin and neocarzinostatin. Biochem Biophys Res Commun. 1980 May 14;94(1):255–261. doi: 10.1016/s0006-291x(80)80214-2. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES