DNA binding of an organic dppz-based intercalator

Biochemistry. 2004 Nov 2;43(43):13657-65. doi: 10.1021/bi049146r.

Abstract

An improved synthesis of a water-soluble derivative of dipyrido[3,2-a:2',3'-c]phenazine (dppz) is reported. The structures of both dppz and the cation ethylene-bipyridyldiylium-phenazine dinitrate [[1][(PF(6))(2)]] have been obtained via X-ray crystallography. Metal complex derivatives of dppz are very well studied. However, using the water soluble [1][(NO(3))(2)], the nature of the interaction of a simple dppz unit with duplex DNA has been investigated for the first time. In both organic solvents and water, 1 displays unstructured luminescence, assigned to an intramolecular charge transfer. The emission is quenched on binding to natural and synthetic duplex DNA, including poly(dA).poly(dT). A variety of techniques reveal that the cation binds to DNA with an affinity comparable to those of many metal dppz complexes, via an intercalative binding mode.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Calorimetry
  • Crystallography, X-Ray
  • DNA / chemistry*
  • Fluorescence Polarization
  • Intercalating Agents / chemistry*
  • Luminescent Measurements
  • Nuclear Magnetic Resonance, Biomolecular
  • Phenazines / chemistry*
  • Polyribonucleotides / chemistry
  • Spectrometry, Fluorescence
  • Spectrometry, Mass, Fast Atom Bombardment
  • Structure-Activity Relationship
  • Thermodynamics*
  • Viscosity

Substances

  • Intercalating Agents
  • Phenazines
  • Polyribonucleotides
  • dipyrido(3,2-a-2',3'-c)phenazine
  • DNA
  • calf thymus DNA