title: Conformationally restricted isoindoline-derived spin labels in duplex DNA: distances and rotational flexibility by pulsed electron-electron double resonance spectroscopy.
abstract: Three structurally related isoindoline-derived spin labels that have different mobilities were incorporated into duplex DNA to systematically study the effect of motion on orientation-dependent pulsed electron-electron double resonance (PELDOR) measurements. To that end, a new nitroxide spin label, (ExIm)U, was synthesized and incorporated into DNA oligonucleotides. (ExIm)U is the first example of a conformationally unambiguous spin label for nucleic acids, in which the nitroxide N-O bond lies on the same axis as the three single bonds used to attach the otherwise rigid isoindoline-based spin label to a uridine base. Continuous-wave (CW) EPR measurements of (ExIm)U confirm a very high rotational mobility of the spin label in duplex DNA relative to the structurally related spin label (Im)U, which has restricted mobility due to an intramolecular hydrogen bond. The X-band CW-EPR spectra of (ExIm)U can be used to identify mismatches in duplex DNA. PELDOR distance measurements between pairs of the spin labels (Im)U, (Ox)U, and (ExIm)U in duplex DNA showed a strong angular dependence for (Im)U, a medium dependence for (Ox)U, and no orientation effect for (ExIm)U. Thus, precise distances can be extracted from (ExIm)U without having to take orientational effects into account.
authors.affiliation: Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik (Iceland), Fax: (+354)5528911.
authors.forename: Dnyaneshwar B
authors.initials: DB
authors.lastname: Gophane
authors.forename: Burkhard
authors.initials: B
authors.lastname: Endeward
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Prisner
authors.forename: Snorri Th
authors.initials: ST
authors.lastname: Sigurdsson
mesh_terms: D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods; D004583:Electrons; D006860:Hydrogen Bonding; D007211:Indoles / Q000737:chemistry*; D009038:Motion; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D013113:Spin Labels
chemical_list: D007211:Indoles; D009841:Oligonucleotides; D013113:Spin Labels; D004247:DNA
keywords: DEER; EPR spectroscopy; PELDOR; aminoxyl radical; nucleic acids