Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes.
Ontology highlight
ABSTRACT:
SUBMITTER: Stone KM
PROVIDER: S-EPMC2792891 | biostudies-literature | 2008
REPOSITORIES: biostudies-literature
Publications
Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes.
Stone Katherine M KM Townsend Jacqueline E JE Sarver Jessica J Sapienza Paul J PJ Saxena Sunil S Jen-Jacobson Linda L
Angewandte Chemie (International ed. in English) 20080101 52
Similar Datasets
Project description:Cu(II) is an essential element for life but is also associated with numerous and serious medical conditions, particularly neurodegeneration. Structural modeling of crystallization-resistant biological Cu(II) species relies on detailed spectroscopic analysis. Electron paramagnetic resonance (EPR) can, in principle, provide spin hamiltonian parameters that contain information on the geometry and ligand atom complement of Cu(II). Unfortunately, EPR spectra of Cu(II) recorded at the traditional X-band frequency are complicated by (i) strains in the region of the spectrum corresponding to the g(∥) orientation and (ii) potentially very many overlapping transitions in the g(⊥) region. The rapid progress of density functional theory computation as a means to correlate EPR and structure, and the increasing need to study Cu(II) associated with biomolecules in more biologically and biomedically relevant environments such as cells and tissue, have spurred the development of a technique for the extraction of a more complete set of spin hamiltonian parameters that is relatively straightforward and widely applicable. EPR at L-band (1-2 GHz) provides much enhanced spectral resolution and straightforward analysis via computer simulation methods. Herein, the anisotropic spin hamiltonian parameters and the nitrogen coordination numbers for two hitherto incompletely characterized Cu(II)-bound species of a prion peptide complex are determined by analysis of their L-band EPR spectra.
| S-EPMC3150385 | biostudies-literature
Project description:The low-spin cyanide complexes of three Co(II) carbonic anhydrases were investigated by electron paramagnetic resonance (e.p.r.) at 9 and 35GHz. Well-defined and closely axial spectra were obtained only in the absence of oxygen. Several mole equivalents of cyanide were required for complete formation of the complexes in frozen solution, although large excesses caused abstraction of the cobalt. Experiments with [(13)C]cyanide showed that the low-spin complexes contained two CN(-) groups in an environment similar to that of the in-plane ligands in [Co(CN)(5)](3-). A combined e.p.r. and spectrophotometric titration confirmed the presence of two CN(-) ligands. A 5-co-ordinate square pyramidal structure involving three protein ligands was proposed. The dicyanide complex could be oxygenated reversibly, producing a characteristic new e.p.r. spectrum. The O(2) molecule was thought to occupy the remaining octahedral metal site in a formally Co(III) species. The optical spectrum of the dicyanide lacked the prominent d-d bands of the high-spin monocyanide. Both e.p.r. and optical data indicated that the low-spin complex was formed much more fully in frozen solution than at room temperature. Differences in behaviour between the high- and low-activity enzymes suggested some variation in conformational flexibility at the metal binding site.
| S-EPMC1166161 | biostudies-other
Project description:We report an approach that extends the applicability of ultrasensitive force-gradient detection of magnetic resonance to samples with spin-lattice relaxation times (T (1)) as short as a single cantilever period. To demonstrate the generality of the approach, which relies on detecting either cantilever frequency or phase, we used it to detect electron spin resonance from a T (1) = 1 ms nitroxide spin probe in a thin film at 4.2 K and 0.6 T. By using a custom-fabricated cantilever with a 4 microm-diameter nickel tip, we achieve a magnetic resonance sensitivity of 400 Bohr magnetons in a 1 Hz bandwidth. A theory is presented that quantitatively predicts both the lineshape and the magnitude of the observed cantilever frequency shift as a function of field and cantilever-sample separation. Good agreement was found between nitroxide T (1) 's measured mechanically and inductively, indicating that the cantilever magnet is not an appreciable source of spin-lattice relaxation here. We suggest that the new approach has a number of advantages that make it well suited to push magnetic resonance detection and imaging of nitroxide spin labels in an individual macromolecule to single-spin sensitivity.
| S-EPMC2799694 | biostudies-literature
Project description:Double electron-electron resonance (DEER) spectroscopy measures the distribution of distances between two electron spins in the nanometer range, often on doubly spin-labeled proteins, via the modulation of a refocused spin echo by the dipolar interaction between the spins. DEER is commonly conducted under conditions where the polarization of the spins is small. Here, we examine the DEER signal under conditions of high spin polarization, thermally obtainable at low temperatures and high magnetic fields, and show that the signal acquires a polarization-dependent out-of-phase component both for the intramolecular and intermolecular contributions. For the latter, this corresponds to a phase shift of the spin echo that is linear in the pump pulse position. We derive a compact analytical form of this phase shift and show experimental measurements using monoradical and biradical nitroxides at several fields and temperatures. The effect highlights a novel aspect of the fundamental spin physics underlying DEER spectroscopy.
| S-EPMC10583274 | biostudies-literature
Project description:Electron spins in semiconductor quantum dots are good candidates of quantum bits for quantum information processing. Basic operations of the qubit have been realized in recent years: initialization, manipulation of single spins, two qubit entanglement operations, and readout. Now it becomes crucial to demonstrate scalability of this architecture by conducting spin operations on a scaled up system. Here, we demonstrate single-electron spin resonance in a quadruple quantum dot. A few-electron quadruple quantum dot is formed within a magnetic field gradient created by a micro-magnet. We oscillate the wave functions of the electrons in the quantum dots by applying microwave voltages and this induces electron spin resonance. The resonance energies of the four quantum dots are slightly different because of the stray field created by the micro-magnet and therefore frequency-resolved addressable control of each electron spin resonance is possible.
| S-EPMC4994114 | biostudies-literature
Project description:Spin resonance of individual spin centers allows applications ranging from quantum information technology to atomic-scale magnetometry. To protect the quantum properties of a spin, control over its local environment, including energy relaxation and decoherence processes, is crucial. However, in most existing architectures, the environment remains fixed by the crystal structure and electrical contacts. Recently, spin-polarized scanning tunneling microscopy (STM), in combination with electron spin resonance (ESR), allowed the study of single adatoms and inter-atomic coupling with an unprecedented combination of spatial and energy resolution. We elucidate and control the interplay of an Fe single spin with its atomic-scale environment by precisely tuning the phase coherence time T2 using the STM tip as a variable electrode. We find that the decoherence rate is the sum of two main contributions. The first scales linearly with tunnel current and shows that, on average, every tunneling electron causes one dephasing event. The second, effective even without current, arises from thermally activated spin-flip processes of tip spins. Understanding these interactions allows us to maximize T2 and improve the energy resolution. It also allows us to maximize the amplitude of the ESR signal, which supports measurements even at elevated temperatures as high as 4 K. Thus, ESR-STM allows control of quantum coherence in individual, electrically accessible spins.
| S-EPMC5815865 | biostudies-literature
Project description:An extensive set of electron spin resonance spectra was obtained over a wide range of frequencies (9, 95, 170, and 240 GHz) and temperatures (2 to 32 degrees C) to explore the dynamic modes of nitroxide-labeled T4 lysozyme in solution. A commonly used nitroxide side chain (R1), or a methylated analogue with hindered internal motion (R2), was substituted for the native side chain at solvent-exposed helical sites, 72 or 131. The spectra at all four frequencies were simultaneously fit with the slowly relaxing local structure (SRLS) model. Good fits were achieved at all the temperatures. Two principle dynamic modes are included in the SRLS model, the global tumbling of the protein and the internal motion consisting of backbone fluctuations and side chain isomerizations. Three distinct spectral components were required for R1 and two for R2 to account for the spectra at all temperatures. One is a highly ordered and slow motional component, which is observed in the spectra of both R1 and R2; it may correspond to conformers stabilized by interaction with the protein surface. The fraction of this component decreases with increasing temperature and is more populated in the R2 spectra, possibly arising from stronger interaction of the nitroxide ring with the protein surface due to the additional methyl group. The other two components of R1 and the second component of R2 are characterized by fast anisotropic diffusion and relatively low ordering, most likely corresponding to conformers having little or no interactions with nearby residues. Ficoll of different concentrations was added to increase the solution viscosity, thereby slowing down the global tumbling of the protein. A significant effect of Ficoll on the internal motion of an immobilized component was apparent in R2 but not in R1. The ability of such multifrequency studies to separate the effects of faster internal modes of motion from slower overall motions is clearly demonstrated, and its utility in future studies is considered.
| S-EPMC2865245 | biostudies-literature
Project description:Camptothecin (CPT) derivatives are clinically effective poisons of DNA topoisomerase I (Top1) able to form a ternary complex with the Top1-DNA complex. The aim of this investigation was to examine the dynamic aspects of the ternary complex formation by means of site-directed spin labeling electron paramagnetic resonance (SDSL-EPR). Two semisynthetic CPT derivatives bearing the paramagnetic moiety were synthesized, and their biological activity was tested. A 22-mer DNA oligonucleotide sequence with high affinity cleavage site for Top1 was also synthesized. EPR experiments were carried out on modified CPT in the presence of DNA, of Top1, or of both. In the last case, a slow motion component in the EPR signal appeared, indicating the formation of the ternary complex. Deconvolution of the EPR spectrum allowed to obtain the relative drug amounts in the complex. It was also possible to demonstrate that the residence time of CPT "trapped" in the ternary complex is longer than hundreds of microseconds.
| S-EPMC7384355 | biostudies-literature
Project description:We herein investigate the heterobimetallic lantern complexes [PtVO(SOCR)4] as charge neutral electronic qubits based on vanadyl complexes (S = 1/2) with nuclear spin-free donor atoms. The derivatives with R = Me (1) and Ph (2) give highly resolved X-band EPR spectra in frozen CH2Cl2/toluene solution, which evidence the usual hyperfine coupling with the 51V nucleus (I = 7/2) and an additional superhyperfine interaction with the I = 1/2 nucleus of the 195Pt isotope (natural abundance ca. 34%). DFT calculations ascribe the spin density delocalization on the Pt2+ ion to a combination of π and δ pathways, with the former representing the predominant channel. Spin relaxation measurements in frozen CD2Cl2/toluene-d8 solution between 90 and 10 K yield Tm values (1-6 μs in 1 and 2-11 μs in 2) which compare favorably with those of known vanadyl-based qubits in similar matrices. Coherent spin manipulations indeed prove possible at 70 K, as shown by the observation of Rabi oscillations in nutation experiments. The results indicate that the heavy Group 10 metal ion is not detrimental to the coherence properties of the vanadyl moiety and that Pt-VO lanterns can be used as robust spin-coherent building blocks in materials science and quantum technologies.
| S-EPMC10782212 | biostudies-literature
Project description:Molecular organic fluorophores are currently used in organic light-emitting diodes, though non-emissive triplet excitons generated in devices incorporating conventional fluorophores limit the efficiency. This limit can be overcome in materials that have intramolecular charge-transfer excitonic states and associated small singlet-triplet energy separations; triplets can then be converted to emissive singlet excitons resulting in efficient delayed fluorescence. However, the mechanistic details of the spin interconversion have not yet been fully resolved. We report transient electron spin resonance studies that allow direct probing of the spin conversion in a series of delayed fluorescence fluorophores with varying energy gaps between local excitation and charge-transfer triplet states. The observation of distinct triplet signals, unusual in transient electron spin resonance, suggests that multiple triplet states mediate the photophysics for efficient light emission in delayed fluorescence emitters. We reveal that as the energy separation between local excitation and charge-transfer triplet states decreases, spin interconversion changes from a direct, singlet-triplet mechanism to an indirect mechanism involving intermediate states.
| S-EPMC8313702 | biostudies-literature