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. 1988 Aug 25;16(16):7943–7960. doi: 10.1093/nar/16.16.7943

Rh(DIP)3(3+): a shape-selective metal complex which targets cruciforms.

M R Kirshenbaum 1, R Tribolet 1, J K Barton 1
PMCID: PMC338502  PMID: 2843807

Abstract

The coordination complex tris(4,7-diphenylphenanthroline)rhodium(III), Rh(DIP)3(3+), binds to and, upon photoactivation, cleaves both DNA strands near the base of a DNA cruciform. Sites of photoinduced double-stranded DNA cleavage by the rhodium complex map to regions containing cruciforms on closed circular pBR322, pColE1 and phi X174 (replicative form) DNAs. Neither cleavage nor binding by the metal complex, assayed using S1 nuclease, is found on the linear plasmid which lacks the extruded cruciform. High resolution mapping experiments reveal that Rh(DIP)3(3+) cleaves at a specific AT-rich site neighboring the stem of the minor cruciform on pBR322. The primary site of cleavage is found at position 3238 on the 3'-strand and 3250 on the 5'-strand and is remarkably specific. The pattern of cleavage, to one side only of the cruciform stem, indicates an asymmetry in the cruciform structure recognized by the complex. These results suggest that Rh(DIP)3(3+) may provide a useful reagent to probe cruciform sites. In addition, the high degree of specificity found in targeting the cruciform structure with this simple metal complex underscores the utility of shape-selection for the recognition of specific sites on a DNA strand.

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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. Barton J. K., Raphael A. L. Site-specific cleavage of left-handed DNA in pBR322 by lambda-tris(diphenylphenanthroline)cobalt(III). Proc Natl Acad Sci U S A. 1985 Oct;82(19):6460–6464. doi: 10.1073/pnas.82.19.6460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chan P. T., Ohmori H., Tomizawa J., Lebowitz J. Nucleotide sequence and gene organization of ColE1 DNA. J Biol Chem. 1985 Jul 25;260(15):8925–8935. [PubMed] [Google Scholar]
  4. Lilley D. M., Kemper B. Cruciform-resolvase interactions in supercoiled DNA. Cell. 1984 Feb;36(2):413–422. doi: 10.1016/0092-8674(84)90234-4. [DOI] [PubMed] [Google Scholar]
  5. Lilley D. M., Markham A. F. Dynamics of cruciform extrusion in supercoiled DNA: use of a synthetic inverted repeat to study conformational populations. EMBO J. 1983;2(4):527–533. doi: 10.1002/j.1460-2075.1983.tb01458.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Lilley D. M., Palecek E. The supercoil-stabilised cruciform of ColE1 is hyper-reactive to osmium tetroxide. EMBO J. 1984 May;3(5):1187–1192. doi: 10.1002/j.1460-2075.1984.tb01949.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lilley D. M. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468–6472. doi: 10.1073/pnas.77.11.6468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Lilley D. M. The kinetic properties of cruciform extrusion are determined by DNA base-sequence. Nucleic Acids Res. 1985 Mar 11;13(5):1443–1465. doi: 10.1093/nar/13.5.1443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Mei H. Y., Barton J. K. Tris(tetramethylphenanthroline)ruthenium(II): a chiral probe that cleaves A-DNA conformations. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1339–1343. doi: 10.1073/pnas.85.5.1339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Müller B. C., Raphael A. L., Barton J. K. Evidence for altered DNA conformations in the simian virus 40 genome: site-specific DNA cleavage by the chiral complex lambda-tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III). Proc Natl Acad Sci U S A. 1987 Apr;84(7):1764–1768. doi: 10.1073/pnas.84.7.1764. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Platt J. R. POSSIBLE SEPARATION OF INTERTWINED NUCLEIC ACID CHAINS BY TRANSFER-TWIST. Proc Natl Acad Sci U S A. 1955 Mar 15;41(3):181–183. doi: 10.1073/pnas.41.3.181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
  14. Sigal N., Alberts B. Genetic recombination: the nature of a crossed strand-exchange between two homologous DNA molecules. J Mol Biol. 1972 Nov 28;71(3):789–793. doi: 10.1016/s0022-2836(72)80039-1. [DOI] [PubMed] [Google Scholar]
  15. Sinden R. R., Pettijohn D. E. Cruciform transitions in DNA. J Biol Chem. 1984 May 25;259(10):6593–6600. [PubMed] [Google Scholar]
  16. Sluka J. P., Horvath S. J., Bruist M. F., Simon M. I., Dervan P. B. Synthesis of a sequence-specific DNA-cleaving peptide. Science. 1987 Nov 20;238(4830):1129–1132. doi: 10.1126/science.3120311. [DOI] [PubMed] [Google Scholar]
  17. Sullivan K. M., Lilley D. M. Influence of cation size and charge on the extrusion of a salt-dependent cruciform. J Mol Biol. 1987 Jan 20;193(2):397–404. doi: 10.1016/0022-2836(87)90227-0. [DOI] [PubMed] [Google Scholar]
  18. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  19. Sutcliffe J. G. Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3737–3741. doi: 10.1073/pnas.75.8.3737. [DOI] [PMC free article] [PubMed] [Google Scholar]

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