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Pyrazolyl-substituted 1,4-dihydroxybenzene and 1,4-dihydroxynaphthene derivatives have been synthesized by reaction of 1,4-benzoquinone and 1,4-naphthoquinone, respectively, with pyrazole. Cyclovoltammetric measurements have shown that 1,4-benzoquinone possesses the potential to oxidize 2-(pyrazol-1-yl)- and 2,5-bis(pyrazol-1-yl)-1,4-dihydroxybenzene. The 2,5-bis(pyrazol-1-yl)- 1,4-dihydroxybenzene reacts with air to give quantitatively black insoluble 2,5-bis(pyrazol-1-yl)-1,4- quinhydrone. Black crystals of 2,5-bis(pyrazol-1-yl)-1,4-quinhydrone suitable for X-ray diffraction were grown from methanol at ambient temperature (monoclinic C2/c). The poor yields of pyrazolylsubstituted 1,4-dihydroxybenzene and 1,4-dihydroxynaphthene derivatives can be explained by the formation of insoluble black quinhydrons in the reaction of benzoquinone and naphthoquinone with pyrazole. The dianions of 2-(pyrazol-1-yl)- and 2,5-bis(pyrazol-1-yl)-1,4-dihydroxybenzene react with oxygen to give the corresponding semiquinone anions. 2,5-Bis(pyrazol-1-yl)-1,4-benzoquinone shows two reversible one-electron reduction processes in cyclovoltammetric measurements, whereas pyrazolyl-substituted 1,4-dihdroxybenzene and -naphthene derivatives undergo irreversibile electrontransfer processes.
To facilitate the measurement of intramolecular distances in solvated RNA systems, a combination of spin-labeling, electron paramagnetic resonance (EPR), and molecular dynamics (MD) simulation is presented. The fairly rigid spin label 2,2,5,5-tetramethyl-pyrrolin-1-yloxyl-3-acetylene (TPA) was base and site specifically introduced into RNA through a Sonogashira palladium catalyzed crosscoupling on column. For this purpose 5-iodouridine, 5-iodo-cytidine and 2-iodo-adenosine phosphoramidites were synthesized and incorporated into RNA-sequences. Application of the recently developed ACE (R) chemistry presented the main advantage to limit the reduction of the nitroxide to an amine during the oligonucleotide automated synthesis and thus to increase substantially the reliability of the synthesis and the yield of labeled oligonucleotides. 4-Pulse Electron Double Resonance (PELDOR) was then successfully used to measure the intramolecular spin–spin distances in six doubly labeled RNA-duplexes. Comparison of these results with our previous work on DNA showed that A- and B-Form can be differentiated. Using an all-atom force field with explicit solvent, MD simulations gave results in good agreement with the measured distances and indicated that the RNA A-Form was conserved despite a local destabilization effect of the nitroxide label. The applicability of the method to more complex biological systems is discussed.
