Prisner T F, Marko A, Sigurdsson S Th
Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
J Magn Reson. 2015 Mar;252:187-98. doi: 10.1016/j.jmr.2014.12.008. Epub 2015 Jan 20.
Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.
核酸分子可以呈现多种结构，并表现出很大程度的构象灵活性，以在细胞中履行其各种功能。在此，我们描述了如何使用脉冲电子-电子双共振（PELDOR或DEER）来研究已掺入两个胞嘧啶类似物作为自旋探针的核酸分子。由于这些新型自旋标记是刚性的，并被掺入双链DNA和RNA分子中，自旋标记本身不存在额外的灵活性。因此，两个自旋标记之间的磁偶极-偶极相互作用编码了自旋标记之间的距离以及相互取向。所有这些信息都可以通过多频/多场PELDOR实验提取，该实验能给出有关核酸分子结构和构象灵活性的非常精确且有价值的信息。我们详细描述了获得构象集合的过程，并通过测试示例和对双链DNA的应用展示了其准确性和局限性。
