Skip to main content
NCBI 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
. 1992 May 15;89(10):4608–4612. doi: 10.1073/pnas.89.10.4608

Cleavage behavior of calicheamicin gamma 1 and calicheamicin T.

S Walker 1, R Landovitz 1, W D Ding 1, G A Ellestad 1, D Kahne 1
PMCID: PMC49132  PMID: 1584797

Abstract

Calicheamicin gamma 1 is a potent antitumor antibiotic that cleaves DNA with a high degree of specificity; there is much interest in the recognition process. We have investigated the DNA-cleaving properties of calicheamicin T, a truncated derivative of calicheamicin. We show that calicheamicin T cleaves DNA in a double-stranded fashion, indicating that the first two sugars are sufficient to facilitate binding of the aglycone in the minor groove. However, calicheamicin T cleaves DNA nonselectivity. This result suggests that cyclization kinetics do not determine the cleavage specificity of the intact drug. Instead, cleavage specificity probably reflects binding specificity. Because of the recognition sites reported in the original cleavage paper, calicheamicin has been assumed to recognize oligopyrimidine DNA sequences containing G-C base pairs. We show here that calicheamicin also cuts efficiently at A.T tracts, sometimes in preference to G.C-rich homopyrimidine tracts. Crystallographic data and experiments with chemical probes indicate that DNA sequences including G.C base pairs have significantly different local conformations from DNA sequences containing several (four or more) sequential A.T base pairs. This difference makes it unlikely that calicheamicin simply senses inherent groove conformation and suggests that there is some degree of "induced fit." The ability to recognize both A.T- and G.C-rich oligopyrimidine sequences with a high degree of specificity makes calicheamicin an unusual minor-groove binder.

Full text

PDF
4608

Images in this article

4609Image
on p.4609
4610Image
on p.4610
4610Image
on p.4610

Selected References

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

  1. Barton J. K. Metals and DNA: molecular left-handed complements. Science. 1986 Aug 15;233(4765):727–734. doi: 10.1126/science.3016894. [DOI] [PubMed] [Google Scholar]
  2. Burkhoff A. M., Tullius T. D. The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell. 1987 Mar 27;48(6):935–943. doi: 10.1016/0092-8674(87)90702-1. [DOI] [PubMed] [Google Scholar]
  3. Chen C. H., Sigman D. S. Chemical conversion of a DNA-binding protein into a site-specific nuclease. Science. 1987 Sep 4;237(4819):1197–1201. doi: 10.1126/science.2820056. [DOI] [PubMed] [Google Scholar]
  4. Dervan P. B. Design of sequence-specific DNA-binding molecules. Science. 1986 Apr 25;232(4749):464–471. doi: 10.1126/science.2421408. [DOI] [PubMed] [Google Scholar]
  5. Drak J., Iwasawa N., Danishefsky S., Crothers D. M. The carbohydrate domain of calicheamicin gamma I1 determines its sequence specificity for DNA cleavage. Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7464–7468. doi: 10.1073/pnas.88.17.7464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Drew H. R., Travers A. A. DNA structural variations in the E. coli tyrT promoter. Cell. 1984 Jun;37(2):491–502. doi: 10.1016/0092-8674(84)90379-9. [DOI] [PubMed] [Google Scholar]
  7. Gao X. L., Patel D. J. Solution structure of the chromomycin-DNA complex. Biochemistry. 1989 Jan 24;28(2):751–762. doi: 10.1021/bi00428a051. [DOI] [PubMed] [Google Scholar]
  8. Hawley R. C., Kiessling L. L., Schreiber S. L. Model of the interactions of calichemicin gamma 1 with a DNA fragment from pBR322. Proc Natl Acad Sci U S A. 1989 Feb;86(4):1105–1109. doi: 10.1073/pnas.86.4.1105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Jencks W. P. On the attribution and additivity of binding energies. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4046–4050. doi: 10.1073/pnas.78.7.4046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Konishi M., Ohkuma H., Matsumoto K., Tsuno T., Kamei H., Miyaki T., Oki T., Kawaguchi H., VanDuyne G. D., Clardy J. Dynemicin A, a novel antibiotic with the anthraquinone and 1,5-diyn-3-ene subunit. J Antibiot (Tokyo) 1989 Sep;42(9):1449–1452. doi: 10.7164/antibiotics.42.1449. [DOI] [PubMed] [Google Scholar]
  11. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  12. Kopka M. L., Yoon C., Goodsell D., Pjura P., Dickerson R. E. The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc Natl Acad Sci U S A. 1985 Mar;82(5):1376–1380. doi: 10.1073/pnas.82.5.1376. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lloyd R. S., Haidle C. W., Robberson D. L. Bleomycin-specific fragmentation of double-stranded DNA. Biochemistry. 1978 May 16;17(10):1890–1896. doi: 10.1021/bi00603a014. [DOI] [PubMed] [Google Scholar]
  14. Long B. H., Golik J., Forenza S., Ward B., Rehfuss R., Dabrowiak J. C., Catino J. J., Musial S. T., Brookshire K. W., Doyle T. W. Esperamicins, a class of potent antitumor antibiotics: mechanism of action. Proc Natl Acad Sci U S A. 1989 Jan;86(1):2–6. doi: 10.1073/pnas.86.1.2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. McCarthy J. G., Williams L. D., Rich A. Chemical reactivity of potassium permanganate and diethyl pyrocarbonate with B DNA: specific reactivity with short A-tracts. Biochemistry. 1990 Jun 26;29(25):6071–6081. doi: 10.1021/bi00477a027. [DOI] [PubMed] [Google Scholar]
  16. Pjura P. E., Grzeskowiak K., Dickerson R. E. Binding of Hoechst 33258 to the minor groove of B-DNA. J Mol Biol. 1987 Sep 20;197(2):257–271. doi: 10.1016/0022-2836(87)90123-9. [DOI] [PubMed] [Google Scholar]
  17. Povirk L. F., Wübter W., Köhnlein W., Hutchinson F. DNA double-strand breaks and alkali-labile bonds produced by bleomycin. Nucleic Acids Res. 1977 Oct;4(10):3573–3580. doi: 10.1093/nar/4.10.3573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Seeman N. C., Rosenberg J. M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. doi: 10.1073/pnas.73.3.804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sigman D. S., Chen C. H. Chemical nucleases: new reagents in molecular biology. Annu Rev Biochem. 1990;59:207–236. doi: 10.1146/annurev.bi.59.070190.001231. [DOI] [PubMed] [Google Scholar]
  20. Sugiura Y., Uesawa Y., Takahashi Y., Kuwahara J., Golik J., Doyle T. W. Nucleotide-specific cleavage and minor-groove interaction of DNA with esperamicin antitumor antibiotics. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7672–7676. doi: 10.1073/pnas.86.20.7672. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sullivan J. K., Lebowitz J. Differential sequence dynamics of homopolymeric and alternating AT tracts in a small plasmid DNA. Biochemistry. 1991 Mar 12;30(10):2664–2673. doi: 10.1021/bi00224a015. [DOI] [PubMed] [Google Scholar]
  22. Yanagi K., Privé G. G., Dickerson R. E. Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J Mol Biol. 1991 Jan 5;217(1):201–214. doi: 10.1016/0022-2836(91)90620-l. [DOI] [PubMed] [Google Scholar]
  23. Zein N., Poncin M., Nilakantan R., Ellestad G. A. Calicheamicin gamma 1I and DNA: molecular recognition process responsible for site-specificity. Science. 1989 May 12;244(4905):697–699. doi: 10.1126/science.2717946. [DOI] [PubMed] [Google Scholar]
  24. Zein N., Sinha A. M., McGahren W. J., Ellestad G. A. Calicheamicin gamma 1I: an antitumor antibiotic that cleaves double-stranded DNA site specifically. Science. 1988 May 27;240(4856):1198–1201. doi: 10.1126/science.3240341. [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