A pulsed EPR method to determine distances between paramagnetic centers with strong spectral anisotropy and radicals: the dead-time free RIDME sequence

J Magn Reson. 2009 Nov;201(1):48-56. doi: 10.1016/j.jmr.2009.08.008. Epub 2009 Aug 15.


Methods to determine distances between paramagnetic metal centers and radicals are scarce. This is unfortunate because paramagnetic metal centers are frequent in biological systems and so far have not been employed much as distance markers. Successful pulse sequences that directly target the dipolar interactions cannot be applied to paramagnetic metal centers with fast relaxation rates and large g-anisotropy, if no echos can be detected and the excitation bandwidth is not sufficient to cover a sufficiently large part of the spectrum. The RIDME method Kulik et al. (2002) [20] circumvents this problem by making use of the T(1)-induced spin-flip of the transition-metal ion. Designed to measure distance between such a fast relaxing metal center and a radical, it suffers from a dead time problem. We show that this is severe because the anisotropy of the metal center broadens the dipolar curves, which therefore, only can be analyzed if the full curve is known. Here, we introduce five-pulse RIDME (5p-RIDME) that is intrinsically dead-time free. Proper functioning of the sequence is demonstrated on a nitroxide biradical. The distance between a low-spin Fe(III) center and a spin label in spin-labeled cytochrome f shows the complete dipolar trace of a transition-metal ion center and a spin label, yielding the distance expected from the structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Anisotropy
  • Bacterial Proteins
  • Cytochromes f / genetics
  • Cytochromes f / metabolism
  • Electron Spin Resonance Spectroscopy / methods*
  • Free Radicals / chemistry*
  • Mutagenesis
  • Nitrogen Oxides / analysis
  • Nostoc / genetics
  • Plasmids / genetics
  • Reference Standards
  • Spin Labels


  • Bacterial Proteins
  • Free Radicals
  • Nitrogen Oxides
  • Spin Labels
  • Cytochromes f