title: Triarylmethyl Labels: Toward Improving the Accuracy of EPR Nanoscale Distance Measurements in DNAs.
abstract: Triarylmethyl (trityl, TAM) based spin labels represent a 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 3. 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 the narrow EPR line of TAM. Distance distributions in nitroxide/nitroxide pairs are influenced by the structure of the linker: the use of a short amine-based linker improves the accuracy by a factor of 2. At the same time, a negligible dependence on the linker length is found for the 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.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Georgiy Yu
authors.initials: GY
authors.lastname: Shevelev
authors.affiliation: International Tomography Center, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Olesya A
authors.initials: OA
authors.lastname: Krumkacheva
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Lomzov
authors.affiliation: N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Kuzhelev
authors.affiliation: N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Dmitry V
authors.initials: DV
authors.lastname: Trukhin
authors.affiliation: N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Olga Yu
authors.initials: OY
authors.lastname: Rogozhnikova
authors.affiliation: N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Victor M
authors.initials: VM
authors.lastname: Tormyshev
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Pyshnyi
authors.affiliation: International Tomography Center, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Matvey V
authors.initials: MV
authors.lastname: Fedin
authors.affiliation: N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Elena G
authors.initials: EG
authors.lastname: Bagryanskaya
mesh_terms: D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D015394:Molecular Structure; D053758:Nanoparticles / Q000737:chemistry*; D014320:Triphenylmethyl Compounds / Q000737:chemistry*
chemical_list: D014320:Triphenylmethyl Compounds; D004247:DNA