Protocol abstract
Nature Protocols 2, - 2354 - 2365 (2007)
Published online: 27 September 2007 | doi:10.1038/nprot.2007.308
Subject Category: Spectroscopy and structural analysis
Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe
Peter Z Qin1,2, Ian S Haworth3, Qi Cai1, Ana K Kusnetzow4, Gian Paola G Grant1, Eric A Price2, Glenna Z Sowa1, Anna Popova1, Bruno Herreros1 & Honghang He1
Abstract
This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron–electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes.
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA.
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0744, USA.
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA.
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
Correspondence to: Peter Z Qin1,2 e-mail: pzq@usc.edu
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