Interaction of distamycin A and netropsin with quadruplex and duplex structures: a comparative 1H-NMR study

Nucleosides Nucleotides Nucleic Acids. 2002;21(8-9):535-45. doi: 10.1081/NCN-120015067.


Homonuclear NMR techniques have been used to investigate the interactions of the minor groove binding agents distamycin A (Dist-A) and the related drug netropsin (Net) with three quadruplexes characterized by different groove widths: [d(TGGGGT)]4 (Q1), [d(GGGGTTTTGGGG)]2 (Q2), and d(GGGGTTGGGGTGTGGGGTTGGGG) (Q3). Netropsin has been found to be in a fast chemical exchange with all three kinds of quadruplexes, whereas Dist-A interacts tightly with Q1 and, at a less extent, with Q2. In order to determine the degree of selectivity of Dist-A for two- rather than four-stranded DNA, we titrated with Dist-A an equimolar solution of Ql and the duplex d(CGCAAATTTGCG)2 (D). This comparative 1H-NMR study allowed us to conclude that Dist-A and, consequently, Net possess higher affinity for duplex DNA.

Publication types

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

MeSH terms

  • Base Composition
  • Binding Sites
  • DNA / chemistry*
  • Distamycins / chemistry*
  • G-Quadruplexes
  • Models, Molecular
  • Molecular Structure
  • Netropsin / chemistry*
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation / drug effects*
  • Protons
  • Structure-Activity Relationship


  • Distamycins
  • Protons
  • Netropsin
  • stallimycin
  • DNA