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Conformationally Restricted Isoindoline‐Derived Spin Labels in Duplex DNA: Distances and Rotational Flexibility by Pulsed Electron–Electron Double Resonance Spectroscopy
Author(s) -
Gophane Dnyaneshwar B.,
Endeward Burkhard,
Prisner Thomas F.,
Sigurdsson Snorri Th.
Publication year - 2014
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201403726
Subject(s) - electron paramagnetic resonance , isoindoline , chemistry , duplex (building) , nitroxide mediated radical polymerization , site directed spin labeling , intramolecular force , crystallography , spin label , resonance (particle physics) , dna , stereochemistry , nuclear magnetic resonance , atomic physics , physics , medicinal chemistry , organic chemistry , biochemistry , radical polymerization , copolymer , polymer
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 NO 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.