Sequence-Specific Spin Labeling of Oligothymidylates by Phosphotriester Chemistry

Oligothymidylates (oligo(dT)'s) with the sequence-specifically-incorporated one-atom-tethered C(5)-nitio-xide-labeled nucleoside 1 were synthesized by the phosphotriester method. Some modifications of the protocol were required to account for the chemical reactivity of the nitroxide, the stability of which was monitored during the synthesis by electron paramagnetic resonance (EPR) spectroscopy. The EPR specific activity (A_EPR) of the FPLC-purified nitroxide-labeled oligomers was determined and found to be in agreement with enzymatically prepared spin-labeled nucleic acids. Annealing the nitroxide-labeled oligo(dT)'s to (dA)_n or oligo(dA) resulted in different EPR-lineshape changes suggesting a strong coupling of the short-tethered nitroxide to global macro-molecular motion.