Journal of magnetic resonance最新文献

{"title":"Probing rare and short-lived conformational states in nucleic acids using off-resonance carbonyl and guanidino carbon R1ρ relaxation dispersion","authors":"Supriya Pratihar ,&nbsp;Yeongjoon Lee ,&nbsp;Ainan Geng ,&nbsp;Shibani Bhattacharya ,&nbsp;Hashim M. Al-Hashimi","doi":"10.1016/j.jmr.2025.107910","DOIUrl":"10.1016/j.jmr.2025.107910","url":null,"abstract":"<div><div>Chemical exchange-based NMR techniques provide powerful approaches for characterizing lowly-populated and short-lived conformational states in nucleic acids. Among possible probes, the nucleobase carbonyl and guanidino carbons stand out due to the sensitivity of their chemical shifts to hydrogen bonding and keto–enol tautomerization. However, chemical exchange measurements targeting these carbon nuclei have not yet been reported in studies of nucleic acids. Here, we present an experiment for measuring off-resonance <em>R</em>_1ρ relaxation dispersion for guanine-C2, guanine-C6, thymine/uracil-C2, and thymine/uracil-C4 carbons in uniformly ¹³C/¹⁵N labeled nucleic acids. We demonstrate the utility of the experiment by characterizing chemical exchange in a G•T mismatch in duplex DNA between a dominant wobble conformation and two lowly-populated, short-lived, and rapidly interconverting Watson–Crick-like tautomeric states (G^enol•T ⇌ G•T^enol) implicated in DNA replicative errors. The population and exchange rate deduced from the guanine-C6, guanine-C2, and thymine-C4 off-resonance <em>R</em>_1ρ relaxation dispersion profiles were in excellent agreement with counterparts obtained from <em>R</em>_1ρ measurements on proton-bound carbon and nitrogen nuclei. The carbon chemical shifts of the minor state were downfield shifted relative to the wobble ground state, consistent with (G)C6 = O···HO-C4(T^enol) and (G^enol)C6-OH···O=C4(T) hydrogen bonding in the Watson-Crick-like tautomeric state. As a second application, we did not detect any exchange contribution to uracil-C2 and uracil-C4 <em>R</em>_1ρ profiles measured for a U·U mismatch in RNA, consistent with isomerization between two alternative wobble conformations occurring on the sub-microsecond timescale. These results establish carbonyl and guanidino carbons as valuable probes for chemical exchange measurements of micro-to-millisecond motions in nucleic acids.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"377 ","pages":"Article 107910"},"PeriodicalIF":2.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144204790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of insufficient 31P pulse amplitudes on 13C-detected 31P13C rotational-echo double-resonance measurements in solid state NMR","authors":"Motahareh G. Larimi,&nbsp;Robert Tycko","doi":"10.1016/j.jmr.2025.107908","DOIUrl":"10.1016/j.jmr.2025.107908","url":null,"abstract":"<div><div>We investigate the effects of insufficient ³¹P pulse amplitudes on ¹³C-detected ³¹P<img>¹³C Rotational-Echo Double-Resonance (REDOR) measurements in a 17.5 T magnetic field. Experimental REDOR data on two compounds show that normalized REDOR difference signals <span><math><mi>Δ</mi><mi>S</mi><mo>/</mo><msub><mi>S</mi><mn>0</mn></msub></math></span> are suppressed when the amplitudes of ³¹P π pulse trains are not very large compared with the ³¹P chemical shift anisotropies. This behavior is explained theoretically by an analysis of the effects of imperfections in π pulse rotations due to the orientation-dependent and time-dependent resonance offsets under magic-angle spinning in REDOR measurements. We show that effects of the same pulse imperfections can be observed directly by measurements of an effective relaxation time <span><math><msup><msub><mi>T</mi><mn>1</mn></msub><mi>eff</mi></msup></math></span> for longitudinal ³¹P spin polarization under identical π pulse trains.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"377 ","pages":"Article 107908"},"PeriodicalIF":2.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diamond rotors for high magic angle spinning frequencies","authors":"Lauren Schaffer ,&nbsp;David Preiss ,&nbsp;Ravi Shankar Palani ,&nbsp;Nicholas Wiesner ,&nbsp;Jiaming Liu ,&nbsp;Samuel Strymish ,&nbsp;Salima Bahri ,&nbsp;Sara Linse ,&nbsp;Neil Gershenfeld ,&nbsp;Robert G. Griffin","doi":"10.1016/j.jmr.2025.107909","DOIUrl":"10.1016/j.jmr.2025.107909","url":null,"abstract":"<div><div>Magic Angle Spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy is limited in spectral resolution by the spinning frequency of rotors that hold the analyte. Traditional yttria-stabilized zirconia (YSZ) rotors have mechanical constraints that typically limit spinning frequencies of 0.7 mm rotors to ω_r/2π ∼ 110 kHz. These frequencies are not sufficient to achieve resolution comparable to that of solution NMR, which theoretically requires ω_r/2π &gt; 300 kHz. Building upon prior work that utilized rotary-assisted drilling, we present significant advances in diamond rotor fabrication using a high precision lathe and a centerless laser machining fixture that achieves improved concentricity of the rotor outer and inner diameters and spinning stability. The new crop of diamond rotors, which interface with the Bruker MAS 3 spinning system equivalently or better than commercial rotors, were spun using automatic 0.7 mm profiles. Furthermore, diamond rotors can be emptied and repacked, and we describe a set of 3D-printed centrifuge tools for efficient execution of this process. We evaluate chemical vapor deposition (CVD) versus high-pressure high-temperature (HPHT) diamonds as rotor material and find HPHT preferable. Extended spin stability tests and multidimensional NMR spectra of Aβ₁_–₄₀ demonstrate the robustness and usability of these rotors. These advances pave the way for higher frequency spinning with helium gas in the future, enabling transformative improvements in MAS NMR for biological and material sciences.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"379 ","pages":"Article 107909"},"PeriodicalIF":2.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144570748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the effect of 1H decoupling on 19F longitudinal relaxation and signal line shape in 5-Fluorotryptophan","authors":"Yuki Toyama ,&nbsp;Koh Takeuchi ,&nbsp;Ichio Shimada","doi":"10.1016/j.jmr.2025.107899","DOIUrl":"10.1016/j.jmr.2025.107899","url":null,"abstract":"<div><div>Fluorine 19 (¹⁹F) in aromatic rings serves as a useful spin probe for studying the structure, dynamics, and intermolecular interactions of biomolecules and small-molecule ligands. Although ¹⁹F NMR involving aromatic ¹⁹F probes has a number of applications, quantitative relaxation analyses of these probes remain challenging due to the complexity of ¹H-¹⁹F spin interaction networks. In this study, we investigated ¹H-¹⁹F spin interactions in the 5-fluorotryptophan system, focusing on the effects of ¹H decoupling on ¹⁹F relaxation properties and line shape. We demonstrate that ¹H decoupling significantly slows down the ¹⁹F magnetization recovery process, leading to reduced sensitivity particularly in large proteins. In addition, ¹H decoupling effectively eliminates cross-correlations between ¹⁹F chemical shift anisotropy and ¹H-¹⁹F dipole-dipole interactions, resolving the asymmetric line shape of the aromatic ¹⁹F signal. Through experimental and theoretical analyses of the ¹H-coupled ¹⁹F spin system, we propose a model that explains these relaxation behaviors. Our results offer practical guidelines for optimizing ¹H decoupling schemes in aromatic ¹⁹F probes, thereby expanding the utility of ¹⁹F NMR.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"377 ","pages":"Article 107899"},"PeriodicalIF":2.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PyEPRI: A CPU & GPU compatible python package for electron paramagnetic resonance imaging","authors":"Rémy Abergel ,&nbsp;Sylvain Durand ,&nbsp;Yves-Michel Frapart","doi":"10.1016/j.jmr.2025.107891","DOIUrl":"10.1016/j.jmr.2025.107891","url":null,"abstract":"<div><div>This work presents the PyEPRI package, an open-source Python package for Electron Paramagnetic Resonance Imaging. The PyEPRI package implements low-level operators, like projection and backprojection, involved in Electron Paramagnetic Resonance (EPR) and also high-level advanced algorithms, like total variation based EPR image reconstruction, for end-users. The package is fully implemented in Python and provides both CPU and GPU computation capabilities, through the libraries Numpy, PyTorch and Cupy. This package comes with a detailed documentation, including precise mathematical definitions and many reproducible demonstration examples and tutorials, making it easy for users with no particular expertise on coding image processing algorithms to get started. This package is also highly modular and only relies on standard data types, as such, it can also be easily used by advanced users to develop new algorithms while benefiting from an optimized computing environment and some rigorously tested operators.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"376 ","pages":"Article 107891"},"PeriodicalIF":2.0,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144116455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Easy-to-implement passive shimming approach of Halbach magnet for low-field NMR measurement","authors":"Mengjuan Gao ,&nbsp;Sihui Luo ,&nbsp;Lin Zhu ,&nbsp;Lizhi Xiao ,&nbsp;Huabing Liu ,&nbsp;Guangzhi Liao ,&nbsp;Xinman Lv ,&nbsp;Hao Chen ,&nbsp;Yi Wang","doi":"10.1016/j.jmr.2025.107887","DOIUrl":"10.1016/j.jmr.2025.107887","url":null,"abstract":"<div><div>Halbach magnets have been widely employed to NMR instruments due to their low weight, low cost, and minimal leakage of magnetic field. However, field inhomogeneity remains challenge due to discrete magnet rings and manufacturing deviations of the magnetic elements. This paper aims to address this limitation through an effective passive shimming approach, which is considered the first step toward constructing high-homogeneity magnets because of its non-powered and inherently stable characteristics. We focus on the transverse dipole field generated by Halbach magnets and develop an easily implementable linear programming-genetic algorithm (LP-GA) hybrid optimization approach for passive shimming. Our methodology first employs an equivalent magnetic dipole model to calculate the sensitivity matrix of the shim pieces in the Region of Interest (ROI). Then, the LP-GA hybrid optimization algorithm determines the optimal position, number, and thickness of the shim pieces. By combining shim pieces of three different thicknesses (1 mm, 1.5 mm, and 2 mm), we significantly reduce the field inhomogeneity of a 48 mT Halbach magnet system. The effectiveness of our approach is validated through NMR measurements using water samples with copper sulfate at different concentrations, demonstrating an improvement in field homogeneity from approximately 1229 ppm to 320 ppm. The experimental results confirm that the proposed approach effectively enhances magnetic field homogeneity of low-field Halbach magnet systems and could be applied to shimming various Halbach-like magnet arrays.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"376 ","pages":"Article 107887"},"PeriodicalIF":2.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improve robustness to mismatched sampling rate: An alternating deep low-rank approach for exponential function reconstruction and its biomedical magnetic resonance applications","authors":"Yihui Huang ,&nbsp;Zi Wang ,&nbsp;Xinlin Zhang ,&nbsp;Jian Cao ,&nbsp;Zhangren Tu ,&nbsp;Meijin Lin ,&nbsp;Lv Li ,&nbsp;Xianwang Jiang ,&nbsp;Di Guo ,&nbsp;Xiaobo Qu","doi":"10.1016/j.jmr.2025.107898","DOIUrl":"10.1016/j.jmr.2025.107898","url":null,"abstract":"<div><div>Undersampling accelerates signal acquisition at the expense of introducing artifacts. Removing these artifacts is a fundamental problem in signal processing and this task is also called signal reconstruction. Through modeling signals as the superimposed exponential functions, deep learning has achieved fast and high-fidelity signal reconstruction by training a mapping from the undersampled exponentials to the fully sampled ones. However, the mismatch, such as undersampling rates (25 % vs. 50 %), anatomical region (knee vs. brain), and contrast configurations (PDw vs. T₂w), between the training and target data will heavily compromise the reconstruction. To overcome this limitation, we propose Alternating Deep Low-Rank (ADLR), which combines deep learning solvers and classic optimization solvers. Experimental validation on the reconstruction of synthetic and real-world biomedical magnetic resonance signals demonstrates that ADLR can effectively alleviate the mismatch issue and achieve lower reconstruction errors than state-of-the-art methods.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"376 ","pages":"Article 107898"},"PeriodicalIF":2.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144099376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PP-SNMR measurements using SQUIDs as compact three-component B-field sensors for spatial imaging","authors":"Tobias Splith ,&nbsp;Andreas Chwala ,&nbsp;Thomas Hiller ,&nbsp;Aaron C. Davis ,&nbsp;Raphael Dlugosch ,&nbsp;Ronny Stolz ,&nbsp;Mike Müller-Petke","doi":"10.1016/j.jmr.2025.107888","DOIUrl":"10.1016/j.jmr.2025.107888","url":null,"abstract":"<div><div>We present pre-polarization surface nuclear magnetic resonance (PP-SNMR) measurements performed with a Superconducting QUantum Interference Device (SQUID) magnetometer on water-filled pallet boxes. The SQUID directly detects the three components of the magnetic field (B-field) NMR response, while conventional SNMR experiments would detect its time derivative and most of the time only a single component. Each of the three vector components of the magnetic field NMR response consists of a component oscillating at Larmor frequency and of a non-oscillating component. We extend the general SNMR theory to model the measured signals. For the non-oscillating signal, another magnetic decay with a large amplitude is superimposed on the signal originating from the water-filled boxes, and we were unable to extract the desired signal. For the oscillating signal component, however, we report good agreement between the measured signal and the forward model in amplitude and phase. Measuring all three components of the B-field introduces a sensitivity to lateral inhomogeneities, which we demonstrate by repeating the experiment with one and two emptied boxes.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"376 ","pages":"Article 107888"},"PeriodicalIF":2.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143916808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strong field gradients enable NMR-based diffusion measurements for K+, Mg2+, Cl−, and SO42− ions in biomolecular solutions","authors":"Tianzhi Wang ,&nbsp;Daniel Arcos ,&nbsp;F. David Doty ,&nbsp;B. Montgomery Pettitt ,&nbsp;Junji Iwahara","doi":"10.1016/j.jmr.2025.107890","DOIUrl":"10.1016/j.jmr.2025.107890","url":null,"abstract":"<div><div>NMR-based diffusion measurements of potassium (K⁺), magnesium (Mg²⁺), chloride (Cl⁻), and sulfate (SO₄²⁻) ions have been challenging even though these ions are biologically important. For these ions, the gyromagnetic ratios of the NMR-active nuclei, ³⁹K, ²⁵Mg, ³⁵Cl, and ³³S, are less than 1/10 of the ¹H gyromagnetic ratio, causing a low sensitivity in NMR detection and a low efficiency in NMR dephasing needed for diffusion measurements. These nuclei also undergo rapid longitudinal and transverse NMR relaxation via the quadrupolar mechanism, severely limiting the effectiveness of NMR-based diffusion measurements. Interactions with biomolecules promote the NMR relaxation of these ions, hindering measurements of the ion diffusion. We demonstrate that, despite these challenges, diffusion of K⁺, Mg²⁺, Cl⁻, and SO₄²⁻ ions in biomolecular solutions can be measured accurately and precisely through use of appropriately designed high-field NMR probe hardware that can generate strong field gradients &gt;1000 G/cm. The NMR-based diffusion coefficients measured at 17.6 T for these ions in the absence of biomolecules agreed well with conductivity-based values in the literature. This consistency supports that ion diffusion along the magnetic field is unaffected by the Lorentz force acting on the ions, as previously predicted. Our data on ion diffusion in solutions of proteins and DNA illuminate the effect of electrostatic interactions on the apparent diffusion coefficients of ions. Thus, high-field NMR probe hardware that can generate strong field gradients opens a new avenue to characterize the dynamic behavior of various ions around biomolecules and their effect on biomolecular electrostatics.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"376 ","pages":"Article 107890"},"PeriodicalIF":2.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143916807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of 15N-SABRE hyperpolarization at high pressures and in supercritical fluids","authors":"Xiaoqing Li ,&nbsp;Jacob R. Lindale ,&nbsp;Loren L. Smith ,&nbsp;Warren S. Warren","doi":"10.1016/j.jmr.2025.107876","DOIUrl":"10.1016/j.jmr.2025.107876","url":null,"abstract":"<div><div>Signal Amplification By Reversible Exchange (SABRE) is a parahydrogen-based hyperpolarization technique that can generate orders-of-magnitude larger signals than thermal spin polarization within a minute. However, this method is limited by the availability of parahydrogen to the solution. Previous work demonstrated SABRE-derived ¹H hyperpolarization at pressures up to 200 bar and using liquid carbon dioxide as a solvent. Here, we extend this work to demonstrate heteronuclear (¹⁵N) SABRE hyperpolarization using conventional solvents with hydrogen pressures up to 400 bar as well as the possibility of using supercritical CO₂ as the solvent. We demonstrate that in both modes, ¹⁵N hyperpolarization comparable to SABRE-SHEATH may be achieved, providing a route for future optimization efforts as well as scale-up. We also present first steps towards exploring SABRE hyperpolarization of ¹²⁹Xe.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"375 ","pages":"Article 107876"},"PeriodicalIF":2.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}