title: A PELDOR-based nanometer distance ruler for oligonucleotides.
abstract: A pulsed electron paramagnetic resonance (EPR) spectroscopic ruler for oligonucleotides was developed using a series of duplex DNAs. The spin-labeling is accomplished during solid-phase synthesis of the oligonucleotides utilizing a palladium-catalyzed cross-coupling reaction between 5-iodo-2'-deoxyuridine and the rigid spin-label 2,2,5,5-tetramethyl-pyrrolin-1-yloxyl-3-acetylene (TPA). 4-Pulse electron double resonance (PELDOR) was then used to measure the intramolecular spin-spin distances via the dipolar coupling, yielding spin-spin distances of 19.2, 23.3, 34.7, 44.8, and 52.5 A. Employing a full-atom force field with explicit water, molecular dynamic (MD) simulations on the same spin-labeled oligonucleotides in their duplex B-form gave spin-spin distances of 19.6, 21.4, 33.0, 43.3, and 52.5 A, respectively, in very good agreement with the measured distances. This shows that the oligonucleotides adopt a B-form duplex structure also in frozen aqueous buffer solution. It also demonstrates that the combined use of site-directed spin-labeling, PELDOR experiments, and MD simulations can yield a microscopic picture about the overall structure of oligonucleotides. The technique is also applicable to more complex systems, like ribozymes or DNA/RNA-protein complexes, which are difficult to access by NMR or X-ray crystallography.
authors.affiliation: Institute of Physical and Theoretical Chemistry, Marie-Curie-Strasse 11, J. W. Goethe-University, Frankfurt am Main, Germany. o.schiemann@prisner.de
authors.forename: Olav
authors.initials: O
authors.lastname: Schiemann
authors.forename: Nelly
authors.initials: N
authors.lastname: Piton
authors.forename: Yuguang
authors.initials: Y
authors.lastname: Mu
authors.forename: Gerhard
authors.initials: G
authors.lastname: Stock
authors.forename: Joachim W
authors.initials: JW
authors.lastname: Engels
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Prisner
mesh_terms: D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D002942:Circular Dichroism; D004578:Electron Spin Resonance Spectroscopy / Q000295:instrumentation / Q000379:methods*; D031541:Fluorescence Resonance Energy Transfer; D015394:Molecular Structure; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics; D013113:Spin Labels
chemical_list: D009841:Oligonucleotides; D013113:Spin Labels