C.3.2.6 Ligand binding to d[(TG 4 T)] 4 inside Xenopus oocytes
In order to maximize the chances of visualizing the effect of ligands inside living cells, we need to apply different ligand selection criteria. A good solubility and low toxicity are essential parameters for the selection of ligands. They should also have a high selectivity and affinity for DNA G4 because inside cells an important competition with other partners has to be considered. The broadening of signatures due to tumbling and decreasing of signals as observed in vitro can be more dramatic inside cell and can prevent the appearance of signals. The ligands selected have to show a good conservation of signal intensities in vitro, it does not necessarily mean that signals lost their intensities in vivo, but crowded conditions usually induce a high decrease of signals observed in 2D spectra. To be selected for in cell NMR experiment, a ligand has to induce perceptible changes in vitro. The effects observed in vitro for the three ligands selected are suitable for the study of interactions with d[(TG 4 T)] 4 inside living cells. Such studies may present us with new directions to understand ligand-G4 binding inside cells and improve affinity and specificity of ligands in drug design. For each of the three ligands that we tested, two of such experiments were performed in two different set of batches containing 200 oocytes each. In the first experiment, the G4 was micro-injected inside ~200 oocytes, and later on, the ligand was incorporated inside the NMR tube and left to diffuse freely during equilibrium period of 1h. In addition, a second experiment started with an in vitro incubation between the ligand and the G4 prior to micro-injection of the mixture of G4 and ligand inside oocytes. Additional control experiments for testing the surrounding buffer were performed after each in-cell experiment to identify any leakage from oocytes.
package, is particularly useful for solid state NMR. Several recent studies have
demonstrated that highly accurate evaluation of SS NMR parameters is possible, 5-9 with
most examples coming from Earth sciences and silicates research. Thanks to the availability of more user-friendly quantum chemical software and advances in computational hardware, today this task can be accomplished as never before.
At pH above 4.5, the Ga 13 cation seems to transform into more disordered GaOOH–Ga(OH) 3 precursors (see Sect. 4.2.1) which is manifested by the decrease of Ga–Ga number of neighbors and Ga–Ga distances (see Table 2, the 2 ⫻ 10 ⫺4 Ga solution at pH 5). In this respect, the Ga 13 polycation is less stable than its aluminum analog which could be isolated in crystalline state by precipitation of basic Al sulfates and selenates at OH/Ga ratios higher than 2 (Johansson, 1962a, 1962b). The rapid transformation of Ga 13 observed in this study by EXAFS and NMR spectroscopy, respectively, at pH ⬎ 4.5 at low Ga concentrations (⬍ 0.001 m) and at pH ⬎ 2.9 in more concentrated solutions (ⱖ0.1 m), is likely to proceed via the formation of less ordered bigger polymeric species having significant proportions of tetracoordinated Ga with a similar geometry as in Ga 13 . These polymers are supposed to exist in a very narrow pH range, rapidly forming Ga-hexa-coordinated hydroxide solids. More studies are needed to establish their exact structure and stability. The schematic structures of the Ga hydroxide polymers proposed to form in this study as a func- tion of hydrolysis progress are presented in Fig. 11.
Hydrated calcium pyrophosphates (CPP, Ca 2 P 2 O 7 ·nH 2 O) are a fundamental family of materials among osteoarticular pathologic calcifications. In this contribution, a comprehensive multinuclear NMR (NuclearMagneticResonance) study of four crystalline and two amorphous phases of this family is presented. 1 H, 31 P and 43 Ca MAS (Magic Angle Spinning) NMR spectra were recorded, leading to informative fingerprints characterizing each compound. In particular, different 1 H and 43 Ca solid state NMR signatures were observed for the amorphous phases, depending on the synthetic procedure used. The NMR parameters of the crystalline phases were determined using the GIPAW (Gauge Including Projected Augmented Wave) DFT approach, based on first-principles calculations. In some cases, relaxed structures were found to improve the agreement between experimental and calculated values, demonstrating the importance of proton positions and pyrophosphate local geometry in this particular NMR crystallography approach. Such calculations serve as a basis for the future ab initio modeling of the amorphous CPP phases.
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Abstract NMR spectroscopy allows measurements of very accurate values of equilibrium dissociation constants using chemical shift perturbation methods, provided that the concentrations of the binding partners are known with high precision and accuracy. The accuracy and precision of these experiments are improved if performed using individual capillary tubes, a method enabling full automation of the measurement. We provide here a protocol to set up and perform these experiments as well as a robust method to measure peptide concentrations using tryptophan as an internal standard.
In this paper, we have presented the geometric optimal methods combined with numerical adapted schemes implemented in the HamPath code which lead to cal- culate the optimal control in the NMR-imaging techniques for the blood sample case. Restricting to a single control field, a contrast of 0.466 was obtained for a BS- sequence and a transfer time of 1.5 × min t f , where min t f is the minimum time to
fingerprints characterizing each compound. In particular, different 1 H and 43 Ca solid state NMR signatures
were observed for the amorphous phases, depending on the synthetic procedure used. The NMR param- eters of the crystalline phases were determined using the GIPAW (Gauge Including Projected Augmented Wave) DFT approach, based on first-principles calculations. In some cases, relaxed structures were found to improve the agreement between experimental and calculated values, demonstrating the importance of proton positions and pyrophosphate local geometry in this particular NMR crystallography approach. Such calculations serve as a basis for the future ab initio modeling of the amorphous CPP phases. Statement of significance
Nuclearmagneticresonance (NMR) spectroscopy is a mea- surement technique used to analyze the properties of matter in order to determine its molecular structure and dynamics. In conventional NMR, the data are recorded independently either in terms of longitudinal, T 1 , or transversal, T 2 , relax-
The current NMR system antenna is a bird-cage structure, composed of 16 copper wires ( 2 cm thick and 20 cm height) placed periodically around a circle of 20 cm in diameter. This system provides a RF magnetic field perpendicular to the longitudinal axis of the main magnet. The capacitor tuning for each wire increases the uniformity of the current density along the wire and produces a 50µT dynamic magnetic field with homogeneity of 1%. However, for fluid small volumes of interest, low signal to noise ratio (SNR) is obtained. A high SNR is needed (a gain of 10 is attended) and the RF coil must be able to collect the signal emitted by the nuclei with better sensitivity throughout the volume of interest. Therefore, the coil, which produces the RF magnetic field and detects the emitted signal, must be placed around the sample during the experiment. The orientation of the RF field is not necessarily perpendicular to the magnet field, but the greater is the perpendicular component of the RF magnetic field, the best is the SNR. Furthermore, a compromise appears with the homogeneity and the SNR: the B1 field homogeneity depends on the coil complexity, versus the line width, the line shape, the coil shape, the number of turns while high SNR involves thickness and lossless lines.
Index Terms— Two-dimensional NMR, parameter esti-
mation, high-resolution, damped sinusoids.
Nuclearmagneticresonance (NMR) spectroscopy is a pow- erful technique for determining the structure of matter. Mul- tidimensional NMR data can be modeled as a sum of mul- tidimensional damped sinusoids. In the recent decades, nu- merous high-resolution subspace-based methods have been proposed to estimate the parameters of one-dimensional (1- D) and multidimensional (M-D) signals. For 1-D signals, we can cite the Kumaresan and Tuft approach , matrix pen- cil, ESPRIT, etc. Some method developed for the 2-D case are 2-D TLS-Prony , matrix enhancement and matrix pen- cil (MEMP) , 2-D ESPRIT , multidimensional folding (MDF) , multidimensional embedding (MDE) . Maxi- mum likelihood methods have been shown to achieve the best estimation performance. However they need usually a pro- hibitive computational complexity to obtain the global maxi- mum of the likelihood function. Among the subspace estima- tion approaches mentioned, there are methods that apply only to undamped sinusoids. However, the NMR signals consist of damped sinusoids, therefore, they cannot be used directly.
Figure 9. Percentage of protons detected by the CPMG pulse sequence for the copolymer-silica composites containing different concentrations of template (P123).
By varying the concentration in templating agent (P123), a series of amphiphilic copolymer-silica composite thin films with different degrees of mesoscopic order were synthesized. Firstly, conventional structural characterization methods based on XRD and TEM established that highly ordered mesophases could be observed for a threshold concentration of 40-50 wt% in templating agent. By using carbon and proton monodimensional NMR
In conclusion, this study revealed a modest dose response e ﬀect between dietary DON and plasma glucose measured by NMR. It is plausible that the homeostatic control of insulin could be disturbed by DON, and thus glucose uptake from the peripheral circulation may be restricted. Given the limited number of animals and that the eﬀect only occurred at the highest dose raises some caution as to the relevance to typical human exposures. Plasma DON was also detected and DON was found to be associated with the plasma protein fraction. The nature of the association remains unknown, but is not likely to be a covalent interaction,
Si MAS NMR spectra have been collected on a Avance I Bruker 300 MHz (7.05T) spectrometer operating at a Larmor frequency of 59.5 MHz and using a 4mm Bruker CPMAS at a spinning frequency of 10 kHz. Data were acquired a CPMG pulse sequence 39–41 with a recycle delay of 200s and typically 256 scans. 16 echoes with an echo delay of 6 ms between consecutive 180° pulses were accumulated. They were then summed up and Fourier transformed to obtain the spectra. The spectra are referenced to an external tetrakis(trimethylsilyl)silane (TKS) sample, for which the highest intensity peak was positioned at −9.9 ppm from that of TMS.
metabolic pathways using combined 1 H and 13 C-NuclearMagneticResonance (NMR) spectroscopy, a technique
which allows the study not only of metabolite concentrations but also their de novo synthesis via cell-specific pathways in the brain. : 1 H and 13 C NMR spectroscopy using [1- 13 C] glucose was performed on extracts of frontal
cortex obtained from groups of rats with acute liver failure induced by hepatic devascularization whose body temperature was maintained either at 37°C (normothermic) or 35°C (hypothermic), and appropriate sham-operated controls. At coma stages of encephalopathy in the normothermic acute liver failure animals, glutamine
which corresponds to the combination rule for resistors, having a resistance R k = 1/D k , placed
in series. Using Eq. (7), we obtain the “serial resistors” self-diffusivity D eff SR = 6.5×10 -10 m 2 /s
which drastically underestimates the self-diffusivity of hexane in mFAU observed using PFG NMR (Figure 4). As expected, the effective diffusivities predicted from the fast-exchange and serial resistors models provide upper and lower boundaries for the experimental diffusivity (due to the fact that the linear combination for the fast exchange model favors the fast diffusion contribution while that for the serial resistors model favors the slow diffusion contribution). Interestingly, this result suggests that a reasonable range estimate of the diffusion in hierarchical porous media can be obtained from these two values.
monitor the structural and electronic changes in M-O 2 upon cycling and to obtain valuable insights on the
transition of chemical phases. To this aim, we recently designed an operando cell dedicated to metal-O 2
batteries that enables for O 2 gas to react at the cathode without compromising the NMR experiments. The
electrochemical performance in the Li-O 2 configuration is quite similar to what is expected in the literature
Motivated by this challenging open question, we performed NMR experiments on a high-quality LiCuVO 4 single crystal in pulsed magnetic fields
up to 55 T providing access to the saturation fields not only for H k c, but also for the perpendicular, H k b, orientation. Our measurements of the NMR line position and width allow for a very precise determination of the field dependence of the local distribution of the magnetization near H sat . The spin-nematic state is a homogeneous, field-dependent, longitudinal spin state without any transverse dipolar order, thus corresponding to a field-dependent NMR line position without any change of its width with respect to the saturated phase. Our NMR results in LiCuVO 4 , together with the bulk
2.4 GMR sensors for NMR
2.4.1 Lithographic process
An important work during this thesis was devoted to sensors fabrication. For this, I used some techniques which are specific to the nanotechnologies environment. In the following part, I will explain the different steps for a sensor fabrication. First of all, we must speak about stacks that are used. They are not done by the CEA, but they come from laboratories with whom the CEA collaborates. Theses collaborators are quite numerous but we can mention INESC-MN(Instituto de Engenharia de Sistemas e Computadores – Microsistemas & Nanotechnologias in Lisbon directed by Paolo Fre- itas), TCD (Trinity Coll` ege of Dublin, laboratory CRANN directed by Mike Coey), Naomi-Sensitec a German company situated in the Mainz, or Allegro Microsystem an American firm situated in Mineapolis (USA). We thus received full GMR wafers; ready to be microprocessed into sensors.
230 R. Sidi-Boulenouar et al.: SHS NMR coils 3.4 Numerical resolution aspects
The angle solutions of Eq. (7) are obtained using a numeri- cal resolution tool. Nevertheless, for a large number of vari- ables, the algorithm may converge to an aberrant solution with some angles higher than π/2, which satisfies the har- monic cancellation but does not maximize the magnetic field. Thus, it is recommended in such a case to solve the designed problem using optimization formalism. The objective func- tion will be a compromise between the maximization of the magnetic field production g(u) (left member of the first equa- tion of Eq. 7) and the minimization of function f (u), ensur- ing the cancellation of the harmonics (remaining equations of Eq. 7):