A semi-rigid isoindoline-derived nitroxide spin label for RNA

Post-print (lokagerð höfundar)A new isoindoline-derived benzimidazole nitroxide spin label, ImUm, was synthesized and incorporated into RNA oligoribonucleotides. ImUm is the first example of a conformationally unambiguous spin label for RNA, in which the nitroxide N–O bond lies on the same axis as the single bond used to attach the rigid isoindoline-based spin label to a uridine base. This results in minimal displacement of the nitroxide upon rotation of this single bond, which is a useful property for a label to be used for distance measurements. Continuous-wave (CW) EPR measurements of RNA duplexes containing ImUm indicate a restricted rotation around this single bond, presumably due to an intramolecular hydrogen bond between the benzimidazole N–H and O4 of the uracil. Orientation-selective pulsed electron–electron double resonance (PELDOR, also called double electron–electron resonance, or DEER) distance measurements between two spin labels in two RNA duplexes showed in one case a strong orientation dependence, further confirming the restricted motion of the spin labels in RNA duplexes.S. Th. S. acknowledges financial support from the Icelandic Research Fund (141062-051). T. F. P. acknowledges financial support by the SFB 902 - Molecular Principles of RNA-based Regulation. We thank Dr S. Jonsdottir for assistance in collecting analytical data for structural characterization of the new compounds and Dr Subham Saha for assistance with preparation of this manuscript.Peer reviewe

Conformationally Restricted Isoindoline-Derived Spin Labels in Duplex DNA: Distances and Rotational Flexibility by Pulsed Electron-Electron Double Resonance Spectroscopy

Post-print (lokagerð höfundar)Three structurally related isoindoline-derived spin labels that have different mobilities were incorporated into duplex DNA to systematically study the effect of motion on orientation-dependent pulsed electron-electron double resonance (PELDOR) measurements. To that end, a new nitroxide spin label, U-ExIm, was synthesized and incorporated into DNA oligonucleotides. U-ExIm is the first example of a conformationally unambiguous spin label for nucleic acids, in which the nitroxide N-O bond lies on the same axis as the three single bonds used to attach the otherwise rigid isoindoline- based spin label to a uridine base. Continuous-wave (CW) EPR measurements of U-ExIm confirm a very high rotational mobility of the spin label in duplex DNA relative to the structurally related spin label U-Im, which has restricted mobility due to an intramolecular hydrogen bond. The Xband CW-EPR spectra of U-ExIm can be used to identify mismatches in duplex DNA. PELDOR distance measurements between pairs of the spin labels U-Im, OxU, and U-ExIm in duplex DNA showed a strong angular dependence for U-Im, a medium dependence for OxU, and no orientation effect for U-ExIm. Thus, precise distances can be extracted from U-ExIm without having to take orientational effects into account.S.Th.S. acknowledges financial support from the Icelandic Research Fund (080041023 and 120001021). T. F. P. acknowledges financial support from the German Research Foundation (CRC902: Molecular Principles of RNA-Based Regulation). We thank H. Gustmann and P. Wenk for help in collecting the PELDOR data, Dr. G. Reginsson for simulations of CW-EPR spectra, and Dr. S. Jonsdottir for assistance in collecting analytical data for structural characterization of the compounds that were prepared.Peer reviewe

TPA labelled oligonucleotides for long range distance measurements by EPR

The folding of the RNA and their three-dimensional structure are areas of the great interest of biological and medical research. Besides X-ray, NMR and FRET, Electron Paramagnetic Resonance (EPR) can be applied to elucidate RNA's three-dimensional structure and also the dynamics of the system. Indeed, EPR spectroscopy has already shown to be a powerful technique to characterize the local surrounding of the paramagnetic center in proteins or oligonucleotides(1,2). Pulsed ELectron Double Resonance (PELDOR) enable us to measure long range distances between two nitroxides TPA(1) in DNA(1) and RNA(2) and TEMPA (2 and 2*)(3). The spinlabel was introduced during the solid-phase oligonucleotide synthesis on different nucleobases(4).</p

Probing the heme-pocket structure of the paramagnetic forms of cytoglobin and a distal histidine mutant using electron paramagnetic resonance

International audienceCytoglobin is a vertebrate globin with an as yet unidentified function. In this work, S- and X-band pulsed EPR methods are used to elucidate the heme environment of ferric wild-type human cytoglobin (wt CYGB). The data resolve an earlier conflict between two x-ray diffraction studies, and show that the heme iron is bis-histidine ligated with both Fe-His bonds having comparable strength. Similar X-band EPR techniques are applied to study the heme-pocket environment of the ferric HE7Q mutant of CYGB (HE7Q CYGB). No distal water is found to coordinate to the heme iron contrasting the known metaquo form of the HE7Q mutant of myoglobin. The hyperfine and nuclear-quadrupole couplings of the directly coordinating heme and hisitidine nitrogens in ferric wt CYGB and HE7Q CYGB are derived and compared with known data on other ferric porphyrin compounds and heme proteins. In a final part, X-band CW EPR techniques is used in combination with absorption spectroscopy to investigate the ligation and oxidation state of wt CYGB in E. coli cells over-expressing this globin. Wt CYGB is found predominantly in the F8His-Fe²⁺-E7His form, whereby a small fraction of the protein exhibits the F8His-Fe²⁺-NO form. All present results will be compared in detail with recent studies on neuroglobin, another member of the vertebrate globin family characterized by a bis-histidine coordination of the heme iron in both its ferrous and ferric form