Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block |
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| Authors: | Frank Kaiser Dr Burkhard Endeward Dr Alberto Collauto Dr Ute Scheffer Prof Thomas F Prisner Prof Michael W Göbel |
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| Institution: | 1. Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany;2. Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany |
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| Abstract: | The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility. |
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| Keywords: | nitroxide PELDOR photocaged spin label RNA aptamer secondary structure mapping |
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