Unit

UNIT 7.17 Attachment of Nitroxide Spin Labels to Nucleic Acids for EPR

  1. Olga Romainczyk1,
  2. Xavier Elduque2,
  3. Joachim W. Engels1

Published Online: 1 JUN 2012

DOI: 10.1002/0471142700.nc0717s49

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Romainczyk, O., Elduque, X. and Engels, J. W. 2012. Attachment of Nitroxide Spin Labels to Nucleic Acids for EPR. Current Protocols in Nucleic Acid Chemistry. 49:7.17:7.17.1–7.17.40.

Author Information

  1. 1

    Goethe-Universität, Frankfurt, Germany

  2. 2

    Universitat de Barcelona, Barcelona, Spain

Publication History

  1. Published Online: 1 JUN 2012

Abstract

In addition to X-ray, NMR, and FRET, electron paramagnetic resonance (EPR) can be applied to elucidate the structure of different macromolecular systems and determine local surroundings of paramagnetic centers in DNA and RNA. This technique permits structural characterization as well as dynamic structural changes of macromolecular systems. To do so, free radicals with good stability must be introduced. Here, the site-directed spin labeling of DNA and RNA based on the Sonogashira cross-coupling reaction is described. First, the appropriate building blocks, either 5-iodo-substituted pyrimidine deoxy- or ribo-nucleoside phosphoramidites are prepared and incorporated by solid-phase synthesis. Following this, the protected oligonucleotides are “on column” reacted with the acetylenic nitroxide spin labels and subsequently purified. Applications of this technique for duplexes, hairpins, and riboswitches in vitro and in cell are described. Curr. Protoc. Nucleic Acid Chem. 49:7.17.1-7.17.40. © 2012 by John Wiley & Sons, Inc.

Keywords:

  • site-directed spin labeling (SDSL);
  • nitroxide;
  • on-column synthesis;
  • Sonogashira cross coupling