Conformationally Restricted Isoindoline‐Derived Spin Labels in Duplex DNA: Distances and Rotational Flexibility by Pulsed Electron–Electron Double Resonance Spectroscopy |
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Authors: | Dr Dnyaneshwar B Gophane Dr Burkhard Endeward Prof Thomas F Prisner Prof Snorri Th Sigurdsson |
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Institution: | 1. Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik (Iceland), Fax: (+354)5528911;2. Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany), Fax: (+49)?06979829404 |
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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. |
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Keywords: | EPR spectroscopy nucleic acids PELDOR DEER aminoxyl radical |
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