Resolving the nanometer-scale structure of biomolecules in natural conditions still remains a challenging task. We report the first distance measurement in nucleic acid at physiological temperature using electron paramagnetic resonance (EPR). The model 10-mer DNA duplex has been labeled with reactive forms of triarylmethyl radicals and then immobilized on a sorbent in water solution and investigated by double quantum coherence EPR. We succeeded in development of optimal triarylmethyl-based labels, approach for site-directed spin labeling and efficient immobilization procedure that, working together, allowed us to measure as long distances as ~4.6 nm with high accuracy at 310 K (37 °C).

The nitroxides of 7-azadispiro[5.1.5.2]pentadecane and 7-azadispiro[5.1.5.2]pentadeca-14-ene series have been prepared, including thiol-specific methane thiosulfonate spin label for site-directed spin labeling. The effect of spirocyclohexane moieties on chemical and spectral properties has been studied. The obtained temperature dependencies of electron spin relaxation parameters demonstrate that new nitroxides may be suitable for PELDOR distance measurements at 80-120 K. Moreover, the new nitroxides demonstrated much higher stability toward reduction by ascorbate than spirocyclohexane-substituted nitroxides of piperidine series and showed 1.3-3.14 times lower reduction rates compared to corresponding 2,2,5,5-tetramethyl nitroxides.

Triarylmethyl radicals (trityls, TAMs) represent a relatively new class of spin labels. The long relaxation of trityls at room temperature in liquid solutions makes them a promising alternative for traditional nitroxides. In this work we have synthesized a series of TAMs including perdeuterated Finland trityl (D36 form) , mono-, di-, and tri-ester derivatives of Finland-D36 trityl, deuterated form of OX63, dodeca-n-butyl homologue of Finland trityl, and triamide derivatives of Finland trityl with primary and secondary amines attached. We have studied room-temperature relaxation properties of these TAMs in liquids using pulsed Electron Paramagnetic Resonance (EPR) at two microwave frequency bands. We have found the clear dependence of phase memory time (Tm~T2) on magnetic field: room-temperature Tm values are ~1.5-2.5 times smaller at Q-band (34 GHz, 1.2 T) compared to X-band (9 GHz, 0.3 T). This trend is ascribed to the contribution from g-anisotropy that is negligible at lower magnetic fields but comes into play at Q-band. In agreement with this, while T1~Tm at X-band, we observe T1>Tm at Q-band due to increased contributions from incomplete motional averaging of g-anisotropy. In addition, the viscosity dependence shows that (1/Tm-1/T1) is proportional to the tumbling correlation time of trityls. Based on the analysis of previous data and results of the present work, we conclude that in general situation where spin label is at least partly mobile, X-band is most suitable for application of trityls for room-temperature pulsed EPR distance measurements.

Triarylmethyl (trityl, TAM) based spin labels represent promising alternative to nitroxides for EPR distance measurements in biomolecules. Herewith, we report synthesis and comparative study of series of model DNA duplexes, 5′-spin-labeled with TAMs and nitroxides. We have found that the accuracy (width) of distance distributions obtained by Double Electron-Electron Resonance (DEER/PELDOR) strongly depends on the type of radical. Replacement of both nitroxides by TAMs in the same spin-labeled duplex allows narrowing of the distance distributions by a factor of three. Replacement of one nitroxide by TAM (orthogonal labeling) leads to a less pronounced narrowing, but at the same time gains sensitivity in DEER experiment due to efficient pumping on narrow EPR line of TAM. Distance distributions in nitroxide/nitroxide pairs are influenced by the structure of linker: the use of a short amine-based linker improves the accuracy by a factor of two. At the same time, negligible dependence on the linker length is found for distribution width in TAM/TAM pairs. Molecular dynamics calculations indicate greater conformational disorder of nitroxide labels compared to TAM ones, thus rationalizing the experimentally observed trends. Thereby, we conclude that double spin-labeling using TAMs allows obtaining narrower spin-spin distance distributions and potentially more precise distances between labeling sites compared to traditional nitroxides.