title: Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels.
abstract: Pulse dipole-dipole electron paramagnetic resonance (EPR) spectroscopy (double electron-electron resonance [DEER] or pulse electron-electron double resonance [PELDOR] and double quantum coherence [DQC]) allows for measurement of distances in biomolecules and can be used at low temperatures in a frozen solution. Recently, the possibility of distance measurement in a nucleic acid at a physiological temperature using pulse EPR was demonstrated. In these experiments, triarylmethyl (TAM) radicals with long memory time of the electron spin served as a spin label. In addition, the duplex was immobilized on modified silica gel particles (Nucleosil DMA); this approach enables measurement of interspin distances close to 4.5 nm. Nevertheless, the possible influence of TAM on the structure of a biopolymer under study and validity of the data obtained by DQC are debated. In this paper, a combination of molecular dynamics (MD) and nuclear magnetic resonance (NMR) methods was used for verification of interspin distances measured by the X-band DQC method. NMR is widely used for structural analysis of biomolecules under natural conditions (room temperature and an aqueous solution). The ultraviolet (UV) melting method and thermal series (1)H NMR in the range 5-95 °C revealed the presence of only the DNA duplex in solution at oligonucleotide concentrations 1 μM to 1.1 mM at temperatures below 40 °C. The duplex structures and conformation flexibility of native and TAM-labeled DNA complexes obtained by MD simulation were the same as the structure obtained by NMR refinement. Thus, we showed that distance measurements at physiological temperatures by the X-band DQC method allow researchers to obtain valid structural information on an unperturbed DNA duplex using terminal TAM spin labels.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Lomzov
authors.affiliation: Novosibirsk State University , Novosibirsk 630090, Russia.|N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia.
authors.forename: Eugeniy A
authors.initials: EA
authors.lastname: Sviridov
authors.affiliation: N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Shernuykov
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Georgiy Yu
authors.initials: GY
authors.lastname: Shevelev
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.|Novosibirsk State University , Novosibirsk 630090, Russia.
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Pyshnyi
authors.affiliation: Novosibirsk State University , Novosibirsk 630090, Russia.|N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia.
authors.forename: Elena G
authors.initials: EG
authors.lastname: Bagryanskaya
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D005609:Free Radicals / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation / Q000528:radiation effects; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D012822:Silicon Dioxide / Q000737:chemistry; D013113:Spin Labels; D013696:Temperature; D014466:Ultraviolet Rays
chemical_list: D005609:Free Radicals; D009841:Oligonucleotides; D013113:Spin Labels; D012822:Silicon Dioxide; D004247:DNA