title: Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR.
abstract: Site-directed spin labeling and pulsed electron-electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.
authors.affiliation: Biomedical Sciences Research Complex, Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK.
authors.forename: Gunnar W
authors.initials: GW
authors.lastname: Reginsson
authors.forename: Sandip A
authors.initials: SA
authors.lastname: Shelke
authors.forename: Christophe
authors.initials: C
authors.lastname: Rouillon
authors.forename: Malcolm F
authors.initials: MF
authors.lastname: White
authors.forename: Snorri Th
authors.initials: ST
authors.lastname: Sigurdsson
authors.forename: Olav
authors.initials: O
authors.lastname: Schiemann
mesh_terms: D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D056968:Lac Repressors / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D013113:Spin Labels
chemical_list: D056968:Lac Repressors; D013113:Spin Labels; D004247:DNA