title: Advanced EPR Methods for Studying Conformational Dynamics of Nucleic Acids.
abstract: Pulsed electron paramagnetic resonance (EPR) spectroscopy has become an important tool for structural characterization of biomolecules allowing measurement of the distances between two paramagnetic spin labels attached to a biomolecule in the 2-8 nm range. In this chapter, we will focus on applications of this approach to investigate tertiary structure elements as well as conformational dynamics of nucleic acid molecules. Both aspects take advantage of using specific spin labels that are rigidly attached to the nucleobases, as they allow obtaining not only the distance but also the relative orientation between both nitroxide moieties with high accuracy. Thus, not only the distance but additionally the three Euler angles between both the nitroxide axis systems and the two polar angles of the interconnecting vector with respect to the nitroxide axis systems can be extracted from a single pair of spin labels. To extract all these parameters independently and unambiguously, a set of multifrequency/multifield pulsed EPR experiments have to be performed. We will describe the experimental procedure as well as newly developed spin labels, which are helpful to disentangle all these parameters, and tools which we have developed to analyze such data sets. The procedures and analyses will be illustrated by examples from our laboratory.
authors.affiliation: Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: B
authors.initials: B
authors.lastname: Endeward
authors.affiliation: Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Marko
authors.affiliation: Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
authors.forename: V P
authors.initials: VP
authors.lastname: Denysenkov
authors.affiliation: Department of Chemistry, Science Institute, University of Iceland, Reykjavık, Iceland.
authors.forename: S Th
authors.initials: ST
authors.lastname: Sigurdsson
authors.affiliation: Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany. Electronic address: prisner@chemie.uni-frankfurt.de.
authors.forename: T F
authors.initials: TF
authors.lastname: Prisner
mesh_terms: D000465:Algorithms; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D013113:Spin Labels
chemical_list: D009696:Nucleic Acids; D013113:Spin Labels
keywords: Multifield; Multifrequency; Nucleic acid; Orientation-selective PELDOR; PELDOR; Pulsed EPR; Rigid spin label; Spectroscopy