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.

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

“…Label size can be adjusted to match the desired time scale or concentration regimes in solution. Probed length scales exceed distances measurable by fluorescence resonance energy transfer (51) or spin coupling (52). Importantly for DNA/protein interactions, SAXS with gold nanocrystals provides information on the distribution of distances and not just the average distance, allowing visualization of ensembles and identification of potential substoichiometric fractions (like those observed for MutL; Fig.…”

Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR

“…EPR spectroscopy in combination with SDSL has been shown to be ideally suited to elucidate the conformations and conformational dynamics of biological systems such as proteins, protein complexes, DNA, and RNA under physiological conditions (Hubbell et al 2000;Cai et al 2006;Bordignon and Steinhoff 2007). By means of spin labeled folded DNA or RNA a nanometer distance ruler was developed (Schiemann et al 2003(Schiemann et al , 2004Piton et al 2005), B/A conformational transitions of DNA (Sicoli et al 2008), and DNA damages (Sicoli et al 2009) were studied by double electron-electron resonance (DEER) spectroscopy (Jeschke and Polyhach 2007) showing its high sensitivity toward small structural changes.…”

Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy

“…Especially modern pulsed EPR methods like electron spin echo envelope modulation (ESEEM) (Dikanov and Tsvetkov 1992) and hyperfine sublevel correlation experiments (HYSCORE) (Benetis et al 2002) allow the gathering of information about the type and structure of surrounding ligands of metal centers, whereas pulsed electron double resonance (Schiemann et al 2004) could be used to localize these metal ions in the global context of the RNA fold. However, to be able to apply these methods, the naturally occurring diamagnetic Mg II has to be substituted by the paramagnetic Mn II (S = 5/2, I = 5/2) as done in previous studies on the mHHRz (Horton et al 1998;Schiemann et al 2003).…”