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RNA aptamers are in vitro-selected binding domains that recognize their respective ligand with high affinity and specificity. They are characterized by complex three-dimensional conformations providing preformed binding pockets that undergo conformational changes upon ligand binding. Small molecule-binding aptamers have been exploited as synthetic riboswitches for conditional gene expression in various organisms. In the present study, double electron-electron resonance (DEER) spectroscopy combined with site-directed spin labeling was used to elucidate the conformational transition of a tetracycline aptamer upon ligand binding. Different sites were selected for post-synthetic introduction of either the (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate by reaction with a 4-thiouridine modified RNA or of 4-isocyanato-2,6-tetramethylpiperidyl-N-oxid spin label by reaction with 29-aminouridine modified RNA. The results of the DEER experiments indicate the presence of a thermodynamic equilibrium between two aptamer conformations in the free state and capture of one conformation upon tetracycline binding.

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Das ortsselektive Einbringen (gelb) eines Elektrons in Thymin mithilfe des modifizierten Nucleotids 1 (1→2) wurde zur Untersuchung der Distanzabhängigkeit des Überschusselektronentransfers in DNA genutzt. Das Elektron katalysiert die Spaltung der DNA an einem Thymindimer (rot) und konnte mehrere UV‐induzierte Läsionen in der DNA 3 reparieren.

The synthesis and electron paramagnetic resonance (EPR) spectroscopic properties of three novel aromatic nitroxides and potential DNA intercalators, the carbazole-based 3,6-dimethylcarbazole-9-oxyl, as well as the acridane-based 9-acridanylidenemalonitrile-10-oxyl and 9-ethylacridanylidenecyanoacetate-10-oxyl, are described. The two acridane-based nitroxides can be isolated and are stable in solution as well as in the solid state for several days. Continuous wave X-band EPR measurements and density functional theory (DFT) calculations demonstrated that the spin density is delocalized over the whole molecule in all three cases. Furthermore, the DFT calculations provided insight into the molecular and electronic structures of these nitroxides and yielded hyperfine coupling constants which are in very good agreement with the experimental data allowing therefore an unambiguous assignment of the hyperfine couplings.