Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy.

Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is powerful in structure and dynamics study of biological macromolecules by providing distance distribution information ranging from 1.8 to 6 nm, providing that the biomolecules are site-specifically labeled with paramagnetic tags. However, long distances up to 16 nm have been measured on perdeuterated and spin-labeled proteins in deuterated solvent by PELDOR. Here we demonstrate long-range distance measurement on a large RNA, the 97-nucleotide 3'SL RNA element of the Dengue virus 2 genome, by combining a posttranscriptional site-directed spin labeling method using an unnatural basepair system with RNA perdeuteration by enzymatic synthesis using deuterated nucleotides. The perdeuteration removes the coupling of the electron spins of the nitroxide spin labels from the proton nuclear spin system of the RNA and does extend the observation time windows of PELDOR up to 50 µs. This enables one to determine long distances up to 14 nm for large RNAs and their conformational flexibility.

Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block.

The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.

Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.

Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.

Exhaustively Trichlorosilylated C1 and C2 Building Blocks: Beyond the Müller-Rochow Direct Process.

The Cl--induced heterolysis of the Si-Si bond in Si2Cl6 generates an [SiCl3]- ion as reactive intermediate. When carried out in the presence of CCl4 or Cl2C═CCl2 (CH2Cl2 solutions, room temperature or below), the reaction furnishes the monocarbanion [C(SiCl3)3]- ([A]-; 92%) or the vicinal dianion [(Cl3Si)2C-C(SiCl3)2]2- ([B]2-; 85%) in excellent yields. Starting from [B]2-, the tetrasilylethane (Cl3Si)2(H)C-C(H)(SiCl3)2 (H2B) and the tetrasilylethene (Cl3Si)2C═C(SiCl3)2 (B; 96%) are readily available through protonation (CF3SO3H) or oxidation (CuCl2), respectively. Equimolar mixtures of H2B/[B]2- or B/[B]2- quantitatively produce 2 equiv of the monoanion [HB]- or the blue radical anion [B•]-, respectively. Treatment of B with Cl- ions in the presence of CuCl2 furnishes the disilylethyne Cl3SiC≡CSiCl3 (C; 80%); in the presence of [HMe3N]Cl, the trisilylethene (Cl3Si)2C═C(H)SiCl3 (D; 72%) is obtained. Alkyne C undergoes a [4+2]-cycloaddition reaction with 2,3-dimethyl-1,3-butadiene (CH2Cl2, 50 °C, 3d) and thus provides access to 1,2-bis(trichlorosilyl)-4,5-dimethylbenzene (E1; 80%) after oxidation with DDQ. The corresponding 1,2-bis(trichlorosilyl)-3,4,5,6-tetraphenylbenzene (E2; 83%) was prepared from C and 2,3,4,5-tetraphenyl-2,4-cyclopentadien-1-one under CO extrusion at elevated temperatures (CH2Cl2, 180 °C, 4 d). All closed-shell products were characterized by 1H, 13C{1H}, and 29Si NMR spectroscopy; an EPR spectrum of [ nBu4N][B•] was recorded. The molecular structures of [ nBu4N][A], [ nBu4N]2[B], B, E1, and E2 were further confirmed by single-crystal X-ray diffraction. On the basis of detailed experimental investigations, augmented by quantum-chemical calculations, plausible reaction mechanisms for the formation of [A]-, [B]2-, C, and D are postulated.

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

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.

A preorganized ditopic borane as highly efficient one- or two-electron trap.

Reduction of the bis(9-borafluorenyl)methane 1 with excess lithium furnishes the red dianion salt Li2[1]. The corresponding dark green monoanion radical Li[1] is accessible through the comproportionation reaction between 1 and Li2[1]. EPR spectroscopy on Li[1] reveals hyperfine coupling of the unpaired electron to two magnetically equivalent boron nuclei (a((11)B) = 5.1 ± 0.1 G, a((10)B) = 1.7 ± 0.2 G). Further coupling is observed to the unique B-CH-B bridgehead proton (a((1)H) = 7.2 ± 0.2 G) and to eight aromatic protons (a((1)H) = 1.4 ± 0.1 G). According to X-ray crystallography, the B···B distances continuously decrease along the sequence 1 → [1](•-) → [1](2-) with values of 2.534(2), 2.166(4), and 1.906(3) Å, respectively. Protonation of Li2[1] leads to the cyclic borohydride species Li[1H] featuring a B-H-B two-electron-three-center bond. This result strongly indicates a nucleophilic character of the boron atoms; the reaction can also be viewed as rare example of the protonation of an element-element σ bond. According to NMR spectroscopy, EPR spectroscopy, and quantum-chemical calculations, [1](2-) represents a closed-shell singlet without any spin contamination. Detailed wave function analyses of [1](•-) and [1](2-) reveal strongly localized interactions of the two boron pz-type orbitals, with small delocalized contributions of the 9-borafluorenyl π systems. Overall, our results provide evidence for a direct B-B one-electron and two-electron bonding interaction in [1](•-) and [1](2-), respectively.

Conformationally restricted isoindoline-derived spin labels in duplex DNA: distances and rotational flexibility by pulsed electron-electron double resonance spectroscopy.

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, (ExIm)U, was synthesized and incorporated into DNA oligonucleotides. (ExIm)U 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 (ExIm)U confirm a very high rotational mobility of the spin label in duplex DNA relative to the structurally related spin label (Im)U, which has restricted mobility due to an intramolecular hydrogen bond. The X-band CW-EPR spectra of (ExIm)U can be used to identify mismatches in duplex DNA. PELDOR distance measurements between pairs of the spin labels (Im)U, (Ox)U, and (ExIm)U in duplex DNA showed a strong angular dependence for (Im)U, a medium dependence for (Ox)U, and no orientation effect for (ExIm)U. Thus, precise distances can be extracted from (ExIm)U without having to take orientational effects into account.

Confirmed by X-ray crystallography: the B⋠B one-electron σ bond.

Is one electron sufficient to bring about significant σ bonding between two atoms? The chemist's view on the chemical bond is usually tied to the concept of shared electron pairs, and not too much experimental evidence exists to challenge this firm belief. Whilst species with the unusual one-electron σ-bonding motif between homonuclear atoms have so far been identified mainly by spectroscopic evidence, we present herein the first crystallographic characterization, augmented by a detailed quantum-chemical validation, for a radical anion featuring a B⋅B one-electron-two-center σ bond.

Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR.

Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q(D)) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q(D) site (MSQ(D)) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with (1)H2O/2H2O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ(D) binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in 1H2O and 2H2O samples and by selective detection of the exchanged deuterons using Q-band 2H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b(D). Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q(D) site are discussed, in light of the unusually high thermodynamic stability of MSQ(D).

Implementation and applications of shaped pulses in EPR.

In this review, we describe the application of shaped pulses for EPR spectroscopy. Pulses generated by fast arbitrary waveform generators are mostly used in the field of EPR spectroscopy for broadband (200 MHz-1 GHz) excitation of paramagnetic species. The implementation and optimization of such broadband pulses in existing EPR spectrometers, often designed and optimized for short rectangular microwave pulses, is demanding. Therefore, a major part of this review will describe in detail the implementation, testing and optimization of shaped pulses in existing EPR spectrometers. Additionally, we review applications using such pulses for broadband inversion of longitudinal magnetization as well as for the creation and manipulation of transverse magnetization in the field of dipolar and hyperfine EPR spectroscopy. They demonstrate the great potential of shaped pulses to improve the performance of pulsed EPR experiments. We give a brief theoretical description of shaped pulses and their limitations, especially for adiabatic pulses, most often used in EPR. We believe that this review can on the one hand be of practical use to EPR groups starting to work with such pulses, and on the other hand give readers an overview of the state of the art of shaped pulse applications in EPR spectroscopy.

Structure and dynamics of nucleic acids.

In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids.

Direct evidence for nitrogen ligation to the high stability semiquinone intermediate in Escherichia coli nitrate reductase A.

The membrane-bound heterotrimeric nitrate reductase A (NarGHI) catalyzes the oxidation of quinols in the cytoplasmic membrane of Escherichia coli and reduces nitrate to nitrite in the cytoplasm. The enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (Q(D)) located in the vicinity of the distal heme b(D). Here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed EPR methods. (14)N and (15)N ESEEM and HYSCORE measurements carried out at X-band ( approximately 9.7 GHz) on the wild-type enzyme or the enzyme uniformly labeled with (15)N nuclei reveal an interaction between the semiquinone and a single nitrogen nucleus. The isotropic hyperfine coupling constant A(iso)((14)N) approximately 0.8 MHz shows that it occurs via an H-bond to one of the quinone carbonyl group. Using (14)N ESEEM and HYSCORE spectroscopies at a lower frequency (S-band, approximately 3.4 GHz), the (14)N nuclear quadrupolar parameters of the interacting nitrogen nucleus (kappa = 0.49, eta = 0.50) were determined and correspond to those of a histidine N(delta), assigned to the heme b(D) ligand His-66 residue. Moreover S-band (15)N ESEEM spectra enabled us to directly measure the anisotropic part of the nitrogen hyperfine interaction (T((15)N) = 0.16 MHz). A distance of approximately 2.2 Abetween the carbonyl oxygen and the nitrogen could then be calculated. Mechanistic implications of these results are discussed in the context of the peculiar properties of the menasemiquinone intermediate stabilized at the Q(D) site of NarGHI.

The power of trichlorosilylation: isolable trisilylated allyl anions, allyl radicals, and allenyl anions.

Treatment of hexachloropropene (Cl2C[double bond, length as m-dash]C(Cl)-CCl3) with Si2Cl6 and [nBu4N]Cl (1 : 4 : 1) in CH2Cl2 results in a quantitative conversion to the trisilylated, dichlorinated allyl anion salt [nBu4N][Cl2C[double bond, length as m-dash]C(SiCl3)-C(SiCl3)2] ([nBu4N][1]). Tetrachloroallene Cl2C[double bond, length as m-dash]C[double bond, length as m-dash]CCl2 was identified as the first intermediate of the reaction cascade. In the solid state, [1]- adopts approximate C s symmetry with a dihedral angle between the planes running through the olefinic and carbanionic fragments of [1]- of C[double bond, length as m-dash]C-Si//Si-C-Si = 78.3(1)°. One-electron oxidation of [nBu4N][1] with SbCl5 furnishes the distillable blue radical 1˙. The neutral propene Cl2C[double bond, length as m-dash]C(SiCl3)-C(SiCl3)2H (2) was obtained by (i) protonation of [1]- with HOSO2CF3 (HOTf) or (ii) H-atom transfer to 1˙ from 1,4-cyclohexadiene. Quantitative transformation of all three SiCl3 substituents in 2 to Si(OMe)3 (2 OMe) or SiMe3 (2 Me) substituents was achieved by using MeOH/NMe2Et or MeMgBr in CH2Cl2 or THF, respectively. Upon addition of 2 equiv. of tBuLi, 2 Me underwent deprotonation with subsequent LiCl elimination, 1,2-SiMe3 migration and Cl/Li exchange to afford the allenyl lithium compound Me3Si(Li)C[double bond, length as m-dash]C[double bond, length as m-dash]C(SiMe3)2 (Li[4]), which is an efficient building block for the introduction of Me, SiMe3, or SnMe3 (5) groups. The trisilylated, monochlorinated allene Cl3Si(Cl)C[double bond, length as m-dash]C[double bond, length as m-dash]C(SiCl3)2 (6), was obtained from [nBu4N][1] through Cl--ion abstraction with AlCl3 and rearrangement in CH2Cl2 (1˙ forms as a minor side product, likely because the system AlCl3/CH2Cl2 can also act as a one-electron oxidant).

PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure.

Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spin labels at positions U4-U14, U4-U15, U14-U26, and U15-U26 were unchanged upon neomycin binding which implies that the global stem-loop architecture is preserved in the absence and presence of the ligand. On the basis of our results, we infer that low-temperature PELDOR data unambiguously demonstrate the existence of an enthalpically favorable set of RNA conformations ready to bind the ligand without major global rearrangement.

Liquid state DNP using a 260 GHz high power gyrotron.

Dynamic nuclear polarization (DNP) at high magnetic fields (9.2 T, 400 MHz (1)H NMR frequency) requires high microwave power sources to achieve saturation of the EPR transitions. Here we describe the first high-field liquid-state DNP results using a high-power gyrotron microwave source (20 W at 260 GHz). A DNP enhancement of -29 on water protons was obtained for an aqueous solution of Fremy's Salt; in comparison the previous highest value was -10 using a solid-state microwave power source (maximum power 45 mW). The increased enhancements are partly due to larger microwave saturation and elevated sample temperature. These experimentally observed DNP enhancements, which by far exceed the predicted values extrapolated from low-field DNP experiments, demonstrate experimentally that DNP is possible in the liquid state also at high magnetic fields.

Multiquantum Counting of Trityl Radicals.

We demonstrate a series of multitrityl radical compounds where accurate spin-counting by pulsed electron paramagnetic resonance (EPR) can be achieved at X-band (9 GHz) frequencies, even for molecules with very short and flexible linkers. Multiquantum filter experiments, well-known from NMR, were used to count the number of coupled electron spins in these compounds. The six pulse double quantum filter sequence used in EPR for distance determinations in biradicals was used. Precise phase settings to separate higher quantum coherences were achieved by an arbitrary waveform generator. The trityl radicals have narrow spectral width so that homogeneous excitation of all spins by the pulses is possible. The transversal relaxation times of higher quantum coherences of trityl radicals are sufficiently long to allow their detection. Our results on model compounds show the potential of this approach to determine oligomeric states in protein complexes in their native environment using functionalized trityl spin labels.

Pulsed electron-electron double-resonance determination of spin-label distances and orientations on the tetrameric potassium ion channel KcsA.

Pulsed electron-electron double-resonance (PELDOR) measurements are presented from the potassium ion channel KcsA both solubilized in detergent and reconstituted in lipids. Site-directed spin-labeling using (1-oxyl-2,2,5,5-tetramethyl-3-pyrrolin-3-yl)methyl methanethiosulfonate was performed with a R64C mutant of the protein. The orientations of the spin-labels in the tetramer were determined by PELDOR experiments performed at two magnetic field strengths (0.3 T/X-band and 1.2 T/Q-band) and variable probe frequency. Quantitative simulation of the PELDOR data supports a strongly restricted nitroxide, oriented at an angle of 65 degrees relative to the central channel axis. In general, poorer quality PELDOR data were obtained from membrane-reconstituted preparations compared to soluble proteins or detergent-solubilized samples. One reason for this is the reduced transverse spin relaxation time T(2) of nitroxides due to crowding of tetramers within the membrane that occurs even at low protein to lipid ratios. This reduced T(2) can be overcome by reconstituting mixtures of unlabeled and labeled proteins, yielding high-quality PELDOR data. Identical PELDOR oscillation frequencies and their dependencies on the probe frequency were observed in the detergent and membrane-reconstituted preparations, indicating that the position and orientation of the spin-labels are the same in both environments.

Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP.

Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron-electron double resonance (PELDOR), also known as double electron-electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.

Carr-Purcell Pulsed Electron Double Resonance with Shaped Inversion Pulses.

Pulsed electron paramagnetic resonance (EPR) spectroscopy allows the determination of distances, in the range of 1.5-8 nm, between two spin-labels attached to macromolecules containing protons. Unfortunately, for hydrophobic lipid-bound or detergent-solubilized membrane proteins, the maximum distance accessible is much lower, because of a strongly reduced coherence time of the electron spins. Here we introduce a pulse sequence, based on a Carr-Purcell decoupling scheme on the observer spin, where each π-pulse is accompanied by a shaped sech/tanh inversion pulse applied to the second spin, to overcome this limitation. This pump/probe excitation scheme efficiently recouples the dipolar interaction, allowing a substantially longer observation time window to be achieved. This increases the upper limit and accuracy of distances that can be determined in membrane protein complexes. We validated the method on a bis-nitroxide model compound and applied this technique to the trimeric betaine transporter BetP. Interprotomer distances as long as 6 nm could be reliably determined, which is impossible with the existing methods.

Room temperature quantum coherence in a potential molecular qubit.

The successful development of a quantum computer would change the world, and current internet encryption methods would cease to function. However, no working quantum computer that even begins to rival conventional computers has been developed yet, which is due to the lack of suitable quantum bits. A key characteristic of a quantum bit is the coherence time. Transition metal complexes are very promising quantum bits, owing to their facile surface deposition and their chemical tunability. However, reported quantum coherence times have been unimpressive. Here we report very long quantum coherence times for a transition metal complex of 68 µs at low temperature (qubit figure of merit QM=3,400) and 1 µs at room temperature, much higher than previously reported values for such systems. We show that this achievement is because of the rigidity of the lattice as well as removal of nuclear spins from the vicinity of the magnetic ion.