Suppression of radiation damping for high precision quantitative NMR

Radiation damping at clinical field strength: Characterization and compensation in quantitative measurements

PURPOSE

In any MR experiment, the bulk magnetization acts on itself, caused by the induced current in the RF receiver circuit that generates an oscillating damping field. This effect, known as "radiation damping" (RD), is usually weak and, therefore, unconsidered in MRI, but can affect quantitative studies performed with dedicated coils that provide a high SNR. The current work examined RD in a setup for investigations of small tissue specimens including a quantitative characterization of the spin-coil system.

THEORY AND METHODS

A custom-made Helmholtz coil (radius and spacing 16 mm) was interfaced to a transmit-receive (Tx/Rx) switch with integrated passive feedback for modulation or suppression of RD similar to preamplifier decoupling. Pulse sequences included pulse-width arrays to demonstrate the absence/ presence of RD and difference techniques employing gradient pulses or composite RF pulses to quantify RD effects during free precession and transmission, respectively. Experiments were performed at 3T in small samples of MnCl2 solution.

RESULTS

Significant RD effects may impact RF pulse application and evolution periods. Effective damping time constants were comparable to typical T2 * times or echo spacings in multi-echo sequences. Measurements of the phase relation showed that deviations from the commonly assumed 90° angle between the damping field and the transverse magnetization may occur.

CONCLUSION

Radiation damping may affect the accuracy of quantitative MR measurements performed with dedicated RF coils. Efficient mitigation can be achieved hardware-based or by appropriate consideration in the pulse sequence.

Quantitative NMR using water as internal calibrant

A new quantitative nuclear magnetic resonance (qNMR) method, called qNMRw, using water as the internal calibrant has been developed. Its principles, procedures, calculations, and test results are presented here. It is shown to avoid the difficulties created by moisture present in other reference materials. High precision and accuracy can be achieved with qNMRw. The method can be used for analyzing technical materials, herbicide formulation products, and other types of chemical samples. It can also be used to measure the purity and concentration of materials to be used as quantitation calibrants.

Solvent suppression techniques for coupling of size exclusion chromatography and 1H NMR using benchtop spectrometers at 43 and 62 MHz

The characterisation of polymeric materials in their full complexity of chain length, monomeric composition, branching and functionalization is a tremendous challenge and is best tackled by tailored multi-dimensional coupled analytical and detection techniques. Herein, we focus on the improvement of an affordable but information rich 2D-method for polymer analysis: the online hyphenation of benchtop ¹H NMR spectroscopy with size exclusion chromatography (SEC). The main benefit of this approach is correlated information of chain length (SEC) to chemical composition (¹H NMR). Our setup combines SEC onflow with a benchtop NMR spectrometer at 43 or 62 MHz with chemical shift resolution as a robust detector. A detailed comparison of the two instruments is included considering, that only the 43 MHz instrument is equipped with a dedicated z-gradient enabling pulse sequences such as WET. The main challenge of this method is the very low concentration of species of interest after chromatographic separation. At typical SEC conditions, the analyte dilution is typically more than a factor of 1000:1 in a protonated solvent. Therefore, an efficient solvent signal suppression is needed. In this article, several suppression pulse sequences are explored like WET, WEFT, JNR and a simple one-pulse approach - some for the first time on this hardware. By choosing an optimal method, signal strength ratios of solvent to analyte of 1:1 or better are achievable on flow. To illustrate the broad range of possible applications, three typical cases of analyte to solvent signal proximity (no overlap, partial and full overlap) are discussed using typical polymers (PS, PMMA, PEMA) and solvents (chloroform and THF). For each case, several suppression methods are compared and evaluated using a set of numerical criteria (analyte signal suppression and broadening, solvent signal suppression, remaining solvent signal width).

TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells

Recognition of specific chromatin modifications by distinct structural domains within “reader” proteins plays a critical role in the maintenance of genomic stability. However, the specific mechanisms involved in this process remain unclear. Here we report that the PHD-Bromo tandem domain of tripartite motif-containing 66 (TRIM66) recognizes the unmodified H3R2-H3K4 and acetylated H3K56. The aberrant deletion of Trim66 results in severe DNA damage and genomic instability in embryonic stem cells (ESCs). Moreover, we find that the recognition of histone modification by TRIM66 is critical for DNA damage repair (DDR) in ESCs. TRIM66 recruits Sirt6 to deacetylate H3K56ac, negatively regulating the level of H3K56ac and facilitating the initiation of DDR. Importantly, Trim66-deficient blastocysts also exhibit higher levels of H3K56ac and DNA damage. Collectively, the present findings indicate the vital role of TRIM66 in DDR in ESCs, establishing the relationship between histone readers and maintenance of genomic stability.

TRIM66 protein has an N-terminal tripartite motif and a C-terminal PHD Bromodomain. Here the authors show the specific histone modification recognition of TRIM66-PHD-Bromodomain through crystallography and biochemistry assay, and further reveal that TRIM66 recognition of certain histone modification is important for DNA damage repair in ESCs.

Spatial encoding and spatial selection methods in high-resolution NMR spectroscopy

A family of high-resolution NMR methods share the common concept of acquiring in parallel different sub-experiments in different spatial regions of the NMR tube. These spatial encoding and spatial selection methods were for the most part introduced independently from each other and serve different purposes, but they share common ingredients, often derived from magnetic resonance imaging, and they all benefit from a greatly improved time-efficiency. This review article provides a description of several spatial encoding and spatial selection methods, including single-scan multidimensional experiments (ultrafast 2D NMR, DOSY, Z spectroscopy, inversion recovery and Laplace NMR), pure shift and selective refocusing experiments (including Zangger-Sterk decoupling, G-SERF and PSYCHE), a Z filter, and fast-pulsing slice-selective experiments. Some key elements for spatial parallelisation are introduced and when possible a common framework is used for the analysis of each method. Sensitivity considerations are discussed, and a selection of applications is analysed to illustrate which questions can be answered thanks to spatial encoding and spatial selection methods, and discuss the perspectives for future developments and applications.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

Isotope ratio monitoring by ¹³C NMR spectrometry (irm-¹³C NMR) provides the complete ¹³C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of ¹³C natural abundance values (50‰), irm-¹³C NMR requires a 1‰ accuracy and thus highly quantitative analysis by ¹³C NMR. Until now, the conventional strategy to determine the position-specific abundance x_i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and ¹³C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform ¹³C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative ¹H NMR pulse sequence (named DWET) with a ¹³C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T₁, which forms a serious limitation for irm-¹³C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T₁ variations. Their performance is evaluated on the determination of the ¹³C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-¹³C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

The new face of isotopic NMR at natural abundance

The most widely used method for isotope analysis at natural abundance is isotope ratio monitoring by Mass Spectrometry (irm-MS) which provides bulk isotopic composition in ² H, ¹³ C, ¹⁵ N, ¹⁸ O or ³⁴ S. However, in the 1980s, the direct access to Site-specific Natural Isotope Fractionation by Nuclear Magnetic Resonance (SNIF-NMR^TM ) was immediately recognized as a powerful technique to authenticate the origin of natural or synthetic products. The initial - and still most popular - application consisted in detecting the chaptalization of wines by irm-² H NMR. The approach has been extended to a wide range of methodologies over the last decade, paving the way to a wide range of applications, not only in the field of authentication but also to study metabolism. In particular, the emerging irm-¹³ C NMR approach delivers direct access to position-specific ¹³ C isotope content at natural abundance. After highlighting the application scope of irm-NMR (² H and ¹³ C), this article describes the major improvements which made possible to reach the required accuracy of 1‰ (0.1%) in irm-¹³ C NMR. The last part of the manuscript summarizes the different steps to perform isotope analysis as a function of the sample properties (concentration, peak overlap) and the kind of targeted isotopic information (authentication, affiliation). Copyright © 2016 John Wiley & Sons, Ltd.

Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression

Abundant solvent nuclear spins, such as water protons in aqueous solution, cause radiation damping in NMR experiments. It is important to know how the effect of radiation damping appears in high-resolution protein NMR because macromolecular studies always require very high magnetic field strengths with a highly sensitive NMR probe that can easily cause radiation damping. Here, we show the behavior of water magnetization after a pulsed-field gradient (PFG) using nutation experiments at 900 MHz with a cryogenic probe: when water magnetization is located in the upper hemisphere (having +Z component, parallel to the external magnetic field), dephasing of the magnetization by a PFG effectively suppresses residual water magnetization in the transverse plane. In contrast, when magnetization is located in the lower hemisphere (having -Z component), the small residual transverse component remaining after a PFG is still sufficient to induce radiation damping. Based on this observation, we designed ¹H-¹⁵N HSQC experiments in which water magnetization is maintained in the upper hemisphere, but not necessarily along Z, and compared them with the conventional experiments, in which water magnetization is inverted during the t₁ period. The result demonstrates moderate gain of signal-to-noise ratio, 0-28%. Designing the experiments such that water magnetization is maintained in the upper hemisphere allows shorter pulses to be used compared to the complete water flip-back and, thereby, is useful as a building block of protein NMR pulse programs in solution.