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Ru(phen)(2)dppz(2+) Luminescence: Dependence on DNA Sequences and Groove-Binding Agents.

R. Erik Holmlin1, Eric D. A. Stemp, Jacqueline K. Barton

  • 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125.

Inorganic Chemistry
|October 24, 2001
PubMed
Summary

The metallointercalator Delta-Ru(phen)(2)dppz(2+) preferentially binds to AT-rich DNA sequences. DNA groove binders can displace or coexist with this complex, revealing its binding orientation and sequence specificity.

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Correlating Electron Transport and Molecular Structure in Organic Thin Films This work was supported by the Office of Naval Research, the Defense Advanced Research Project Agency, and the National Science Foundation ECS-97294053. R.E.H. thanks the National Institutes of Health for a postdoctoral fellowship, and R.H. thanks the Deutsche Forschungsgemeinschaft and the BASF fellowship program for financial support. We thank Andreas Terfort for the synthesis of aromatic thiols. Collaboration between Caracas and Evanston is supported by NSF Conicit.

Angewandte Chemie (International ed. in English)·2001

Area of Science:

  • Photochemistry
  • Biophysical Chemistry
  • Molecular Biology

Background:

  • Ruthenium complexes like Ru(phen)(2)dppz(2+) are used as probes for DNA structure.
  • Understanding sequence-specific DNA binding is crucial for drug development and molecular diagnostics.

Purpose of the Study:

  • To investigate the DNA sequence preference of Delta-Ru(phen)(2)dppz(2+).
  • To evaluate the effect of major and minor groove binding agents on the luminescence of the ruthenium complex bound to DNA.

Main Methods:

  • Time-resolved luminescence spectroscopy.
  • DNA binding studies using synthetic polynucleotides (poly d(AT), poly d(GC)) and mixed-sequence DNA.
  • Competitive binding assays with major (Rh complex) and minor (distamycin) groove binders.

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Main Results:

  • Delta-Ru(phen)(2)dppz(2+) shows a preference for AT-rich DNA sequences, binding to approximately 85% of sites in mixed polymers.
  • A major groove rhodium complex displaces Ru(phen)(2)dppz(2+) from DNA, indicating intercalation from the major groove side.
  • Minor groove binder distamycin co-binds with Ru(phen)(2)dppz(2+) on AT-rich DNA, suggesting simultaneous accommodation.

Conclusions:

  • Ru(phen)(2)dppz(2+) exhibits significant sequence selectivity for AT sites in DNA.
  • The photophysical properties of Ru(phen)(2)dppz(2+) can be modulated by groove binders, confirming its intercalation mode and major groove entry.
  • These findings provide insights into metallointercalator-DNA interactions and support NMR-based structural assignments.