title: Interaction of triarylmethyl radicals with DNA termini revealed by orientation-selective W-band double electron-electron resonance spectroscopy.
abstract: Spin labels selectively attached to biomolecules allow high-accuracy nanoscale distance measurements using pulsed electron paramagnetic resonance (EPR), in many cases providing the only access to the structure of complex biosystems. Triarylmethyl (TAM) radicals have recently emerged as a new class of spin labels expanding the applicability of the method to physiological temperatures. Along with other factors, the accuracy of the obtained distances crucially relies on the understanding of interactions between biomolecules and spin labels. In this work, we consider such crucial interactions and their impact on pulsed EPR distance measurements in TAM-labeled DNAs. Using orientation-selective high-frequency (94 GHz) double electron-electron resonance (DEER) we demonstrate strong specific interactions between DNA termini and TAM labels, leading to a significant restriction of their conformational mobility. An understanding of such interactions guides the way to select optimum TAM-labeling strategies, thus refining nanoscale EPR distance measurements in nucleic acids and their complexes under physiological conditions.
authors.affiliation: International Tomography Center SB RAS, Novosibirsk, 630090, Russia. mfedin@tomo.nsc.ru and Novosibirsk State University, Novosibirsk, 630090, Russia.
authors.forename: Matvey V
authors.initials: MV
authors.lastname: Fedin
authors.affiliation: Novosibirsk State University, Novosibirsk, 630090, Russia and Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.
authors.forename: Georgiy Yu
authors.initials: GY
authors.lastname: Shevelev
authors.affiliation: Novosibirsk State University, Novosibirsk, 630090, Russia and Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Pyshnyi
authors.affiliation: Novosibirsk State University, Novosibirsk, 630090, Russia and N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia. egbagryanskaya@nioch.nsc.ru.
authors.forename: Victor M
authors.identifier: http://orcid.org/0000-0003-4975-9993
authors.initials: VM
authors.lastname: Tormyshev
authors.affiliation: Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland. maxim.yulikov@phys.chem.ethz.ch.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Jeschke
authors.affiliation: Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland. maxim.yulikov@phys.chem.ethz.ch.
authors.forename: Maxim
authors.initials: M
authors.lastname: Yulikov
authors.affiliation: Novosibirsk State University, Novosibirsk, 630090, Russia and N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia. egbagryanskaya@nioch.nsc.ru.
authors.forename: Elena G
authors.initials: EG
authors.lastname: Bagryanskaya
mesh_terms: D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D004583:Electrons; D005609:Free Radicals / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013113:Spin Labels
chemical_list: D005609:Free Radicals; D013113:Spin Labels; D004247:DNA