Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Jan 25;19(2):257–264. doi: 10.1093/nar/19.2.257

Sequence-specific cleavage of double-stranded DNA caused by X-ray ionization of the platinum atom in the Pt-bis-netropsin--DNA complex.

S L Grokhovsky 1, V E Zubarev 1
PMCID: PMC333588  PMID: 1849628

Abstract

An analog of the antibiotic netropsin containing two netropsin-like fragments linked covalently via a platinum atom has been synthesized. DNase I and hydroxyl radical footprinting studies have shown that this compound binds at selective sites on a DNA restriction fragment with a known nucleotide sequence. After X-ray irradiation of Pt-bis-netropsin--DNA complexes a platinum-mediated cleavage of DNA is observed at specific DNA sites. This enables one to determine the location of the synthetic ligand on the DNA with a precision of about one nucleotide. The cleavage activity seems to be related to the emission of Auger electrons from the platinum atom that cause rupture of the deoxyribose residues on the two DNA strands near the position of the platinum atom in the complex.

Full text

PDF
257

Images in this article

259Image
on p.259
261Image
on p.261

Selected References

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

  1. Coll M., Aymami J., van der Marel G. A., van Boom J. H., Rich A., Wang A. H. Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. Biochemistry. 1989 Jan 10;28(1):310–320. doi: 10.1021/bi00427a042. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Dickerson R. E., Kopka M. L. Nuclear Overhauser data and stereochemical considerations suggest that netropsin binds symmetrically within the minor groove of poly(dA).poly(dT), forming hydrogen bonds with both strands of the double helix. J Biomol Struct Dyn. 1985 Dec;3(3):423–431. doi: 10.1080/07391102.1985.10508431. [DOI] [PubMed] [Google Scholar]
  4. Galas D. J., Schmitz A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 1978 Sep;5(9):3157–3170. doi: 10.1093/nar/5.9.3157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gursky G. V., Zasedatelev A. S., Zhuze A. L., Khorlin A. A., Grokhovsky S. L., Streltsov S. A., Surovaya A. N., Nikitin S. M., Krylov A. S., Retchinsky V. O. Synthetic sequence-specific ligands. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):367–378. doi: 10.1101/sqb.1983.047.01.043. [DOI] [PubMed] [Google Scholar]
  6. Klevit R. E., Wemmer D. E., Reid B. R. 1H NMR studies on the interaction between distamycin A and a symmetrical DNA dodecamer. Biochemistry. 1986 Jun 3;25(11):3296–3303. doi: 10.1021/bi00359a032. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Kraev A. S. Prostaia sistema klonirovaniia v fage M13 i sekvenirovaniia DNK s terminatorami. Mol Biol (Mosk) 1988 Sep-Oct;22(5):1164–1197. [PubMed] [Google Scholar]
  9. Kuwabara M., Yoon C., Goyne T., Thederahn T., Sigman D. S. Nuclease activity of 1,10-phenanthroline-copper ion: reaction with CGCGAATTCGCG and its complexes with netropsin and EcoRI. Biochemistry. 1986 Nov 18;25(23):7401–7408. doi: 10.1021/bi00371a023. [DOI] [PubMed] [Google Scholar]
  10. Martin R. F., Holmes N. Use of an 125I-labelled DNA ligand to probe DNA structure. 1983 Mar 31-Apr 6Nature. 302(5907):452–454. doi: 10.1038/302452a0. [DOI] [PubMed] [Google Scholar]
  11. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  12. Rill R. L., Marsch G. A., Graves D. E. 7-Azido-actinomycin D: a photoaffinity probe of the sequence specificity of DNA binding by actinomycin D. J Biomol Struct Dyn. 1989 Dec;7(3):591–605. doi: 10.1080/07391102.1989.10508509. [DOI] [PubMed] [Google Scholar]
  13. Shinohara K., Ohara H., Kobayashi K., Maezawa H., Hieda K., Okada S., Ito T. Enhanced killing of HeLa cells pre-labeled with 5-bromodeoxyuridine by monochromatic synchrotron radiation at 0.9 A: an evidence for Auger enhancement in mammalian cells. J Radiat Res. 1985 Sep;26(3):334–338. doi: 10.1269/jrr.26.334. [DOI] [PubMed] [Google Scholar]
  14. Tullius T. D., Dombroski B. A. Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proc Natl Acad Sci U S A. 1986 Aug;83(15):5469–5473. doi: 10.1073/pnas.83.15.5469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Warpehoski M. A., Hurley L. H. Sequence selectivity of DNA covalent modification. Chem Res Toxicol. 1988 Nov-Dec;1(6):315–333. doi: 10.1021/tx00006a001. [DOI] [PubMed] [Google Scholar]
  16. Zasedatelev A. S., Zhuze A. L., Tsimmer K., Grokhovskii S. L., Tumanian V. G. Stereokhimicheskaia model' molekuliarnogo mekhanizma "uznavaniia" AT-par pri sviazyvanii s DNK antibiotikov distamitsina a i netropsina. Dokl Akad Nauk SSSR. 1976 Dec 1;231(4):1006–1009. [PubMed] [Google Scholar]
  17. Zimmer C., Wähnert U. Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Prog Biophys Mol Biol. 1986;47(1):31–112. doi: 10.1016/0079-6107(86)90005-2. [DOI] [PubMed] [Google Scholar]

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

RESOURCES