title: Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.
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.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA. pzq@usc.edu
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
authors.forename: Ian S
authors.initials: IS
authors.lastname: Haworth
authors.forename: Qi
authors.initials: Q
authors.lastname: Cai
authors.forename: Ana K
authors.initials: AK
authors.lastname: Kusnetzow
authors.forename: Gian Paola G
authors.initials: GP
authors.lastname: Grant
authors.forename: Eric A
authors.initials: EA
authors.lastname: Price
authors.forename: Glenna Z
authors.initials: GZ
authors.lastname: Sowa
authors.forename: Anna
authors.initials: A
authors.lastname: Popova
authors.forename: Bruno
authors.initials: B
authors.lastname: Herreros
authors.forename: Honghang
authors.initials: H
authors.lastname: He
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D015336:Molecular Probe Techniques; D009589:Nitrogen Oxides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012984:Software; D013113:Spin Labels
chemical_list: D009589:Nitrogen Oxides; D013113:Spin Labels; D012313:RNA; D004247:DNA; C039900:nitroxyl