Binding of ethidium to DNA measured using a 2D diffusion-modulated gradient COSY NMR experiment

William H. Gmeiner, Christopher J. Hudalla, Ana Maria Soto, Luis Marky

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


The binding of ethidium bromide to a DNA hairpin (dU5-hairpin) was investigated using a novel 2D diffusion-modulated gradient correlation spectroscopy (DMG-COSY) experiment to evaluate the applicability of this technique for studying the binding of drugs to DNA. The DMG-COSY experiment includes a preparation period during which coherent magnetization is attenuated due to molecular self-diffusion. Magnetization then evolves due to scalar coupling during an evolution delay, and is detected using gradient pulses for coherence selection. The time-domain data are processed in an analogous manner as for gradient-selected COSY experiments. The diffusion coefficient for uridine in DMSO solution was determined from the H5-H6 crosspeak intensities for a series of 2D DMG-COSY experiments that differed in the magnitude of the gradient pulses applied during the preparation period of the DMG-COSY experiment. The diffusion coefficient for uridine calculated from the DMG-COSY experiments was identical (within experimental error) to that determined from 1D diffusion experiments (5.24x10-6 cm2/s at 26°C). The diffusion coefficients for ethidium bromide and for the dU5-hairpin were first measured separately using the DMG-COSY experiment, and then measured in the putative complex. The diffusion coefficient for free ethidium bromide (4.15x10-6 cm2/s at 26°C) was considerably larger than for the dU5-hairpin (1.60x10-6 cm2/s at 26°C), as expected for the smaller molecule. The diffusion coefficient for ethidium was markedly decreased upon addition of the dU5-hairpin, consistent with complex formation (1.22x10-6 cm2/s at 26°C). Complex formation of 1:1 stoichiometry between ethidium and the stem of the dU5-hairpin was verified independently by fluorescence spectroscopy. These results demonstrate the utility of the DMG-COSY experiment for investigating the binding of drugs to DNA in aqueous solution. Copyright (C) 2000 Federation of European Biochemical Societies.

Original languageEnglish (US)
Pages (from-to)148-152
Number of pages5
JournalFEBS Letters
Issue number2-3
StatePublished - Jan 14 2000


  • Bipolar pulse pair-longitudinal encode/decode
  • Diffusion
  • Drug-DNA interaction
  • Two-dimensional nuclear magnetic resonance

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology


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