Orientation-selective DEER using rigid spin labels, cofactors, metals, and clusters

The dipolar interaction between two paramagnetic centres depends upon their spin–spin distance and relative orientation. Generally most experiments are carried out under conditions where the DEER signal only reports on the spin–spin distances and, for this type of data, sophisticated analysis methods for obtaining distance distributions have been developed. Recently there have been an increasing number of studies on systems where the DEER signals depend upon both distance and spin pair orientation. These investigations have relied on the use of rigid spin labels (those with a well-defined spatial position) and/or spectrometers operating at Q-band frequencies and above capable of performing DEER experiments with high resolution and sensitivity. In this article we discuss in detail orientation-selective DEER experiments for which the modulation depth and the dipolar frequencies depend on the relative orientation of the two paramagnetic centres and the distance. Analysis of the data in the presence of distance and orientation distributions is discussed, and representative examples from the literature are given for systems containing spin labels, organic cofactors, metals, and metal clusters

A High-Conversion-Factor, Double-Resonance Structure for High-Field Dynamic Nuclear Polarization

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Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances

In this protocol, we describe the facile synthesis of the nitroxide spin-label 2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene (TPA) and then its coupling to DNA/RNA through Sonogashira cross-coupling during automated solid-phase synthesis. Subsequently, we explain how to perform distance measurements between two such spin-labels on RNA/DNA using the pulsed electron paramagnetic resonance method pulsed electron double resonance (PELDOR). This combination of methods can be used to study global structure elements of oligonucleotides in frozen solution at RNA/DNA amounts of similar to 10 nmol. We especially focus on the Sonogashira cross-coupling step, the advantages of the ACE chemistry together with the appropriate parameters for the RNA synthesizer and on the PELDOR data analysis. This procedure is applicable to RNA/DNA strands of up to similar to 80 bases in length and PELDOR yields reliably spin-spin distances up to similar to 6.5 nm. The synthesis of TPA takes similar to 5 days and spin labeling together with purification similar to 4 days. The PELDOR measurements usually take similar to 16 h and data analysis from an hour up to several days depending on the extent of analysis.</p