NMR of insensitive nuclei enhanced by dynamic nuclear polarization

Despite the powerful spectroscopic information it provides, Nuclear Magnetic Resonance (NMR) spectroscopy suffers from a lack of sensitivity, especially when dealing with nuclei other than protons. Even though NMR can be applied in a straightforward manner when dealing with abundant protons of organic molecules, it is very challenging to address biomolecules in low concentration and/or many other nuclei of the periodic table that do not provide as intense signals as protons. Dynamic Nuclear Polarization (DNP) is an important technique that provides a way to dramatically increase signal intensities in NMR. It consists in transferring the very high electron spin polarization of paramagnetic centers (usually at low temperature) to the surrounding nuclear spins with appropriate microwave irradiation. DNP can lead to an enhancement of the nuclear spin polarization by up to four orders of magnitude. We present in this article some basic concepts of DNP, describe the DNP apparatus at EPFL, and illustrate the interest of the technique for chemical applications by reporting recent measurements of the kinetics of complexation of 89Y by the DOTAM ligand.     

Cross-Binding of Adenosine by Aptamers Selected Using Theophylline

We recently reported that some adenosine binding aptamers can also bind caffeine and theophylline with around 20-fold lower affinities. This discovery led to the current work to examine the cross-binding of adenosine to theophylline aptamers. For the DNA aptamer for theophylline, cross-binding to adenosine was observed, and the affinity was 18 to 38-fold lower for adenosine based on assays using isothermal titration calorimetry and ThT fluorescence spectroscopy. The binding complexes were characterized using NMR spectroscopy, and both adenosine and theophylline showed an overall similar binding structure to the DNA theophylline aptamer, although small differences were also observed. In contrast, the RNA aptamer did not show binding to adenosine, although both aptamers have very similar relative selectivity for various methylxanthines including caffeine. After a negative selection, a few new aptamers with completely different primary sequences for theophylline were obtained and they did not show binding to adenosine. Thus, there are many ways for aptamers to bind theophylline and some can have cross-binding to adenosine. In biology, theophylline, caffeine, and adenosine can bind to the same protein receptors to regulate sleep, and their binding to the same DNA motifs may suggest an early role of nucleic acids in similar regulatory functions.     

Thermal oxidative and photo‐oxidative degradation of polytetrahydrofuran studied using 1H NMR, 13C NMR and GPC

The products and mechanism of the thermal oxidative degradation at 180 °C and the photo‐oxidative degradation at 40 °C of polytetrahydrofuran have been investigated using ¹H NMR, ¹³C NMR and GPC. The NMR analysis was assisted by the use of DEPT ¹³C spectra, two‐dimensional NMR spectroscopy (COSY, HMQC and HMBC) and chemical shift simulation software. The NMR spectra of both thermally and photolytically degraded samples were similar showing that the degradation mechanisms were similar. GPC indicated that both chain scission, leading to lower molar mass products, and chain extension, leading to higher molar mass products, occurred initially. NMR analysis of the initial soluble degraded polymers showed that chain scission resulted in formate, aldehyde, propyl ether, butyl ether and propanoyl chain ends, and in‐chain ester groups were also formed. For longer periods of degradation, crosslinked gels were formed but these were not amenable to detailed structural characterisation by high‐resolution NMR to determine the crosslink mechanism. Copyright © 2004 Society of Chemical Industry     

Polarization Transfer from Ligands Hyperpolarized by Dissolution Dynamic Nuclear Polarization for Screening in Drug Discovery

Nuclear magnetic resonance (NMR) spectroscopy is a valuable technique for ligand screening, because it exhibits high specificity toward chemical structure and interactions. Dissolution dynamic nuclear polarization (DNP) is a recent advance in NMR methodology that enables the creation of non‐equilibrium spin states, which can dramatically increase NMR sensitivity. Here, the transfer of such spin polarization from hyperpolarized ligand to protein is observed. Mixing hyperpolarized benzamidine with the serine protease trypsin, a “fingerprint” of enhanced protein signals is observed, which shows a different intensity profile than the equilibrium NMR spectrum of the protein, but coincides closely to the frequency profile of a saturation transfer difference (STD) NMR experiment. The DNP experiment benefits from hyperpolarization and enables observation of all frequencies in a single, rapid experiment. Based on these merits, it is an interesting alternative to the widely used STD experiment for identification of protein–ligand interactions.     

Si and Al MAS NMR characterization of non-hydrated zeolites Y upon adsorption of ammonia

Solid-state NMR characterization of zeolite catalysts in the hydrated state is often accompanied by an uncontrolled hydrolysis of the framework. In the present work it is demonstrated that the limitations occurring for ²⁹Si and ²⁷Al MAS NMR spectroscopy of non-hydrated zeolites Y, such as strong decrease of resolution and significant line broadening, can be overcome by loading these materials with ammonia. In the ²⁹Si MAS NMR spectra of non-hydrated and ammonia-loaded zeolites Y, no dehydration-induced high-field shift of Si(nAl) signals (n = 3, 2, 1) occurs, which is generally responsible for the loss of resolution in the spectra of non-hydrated materials. The ²⁷Al MAS NMR spectra of the non-hydrated and ammonia-loaded zeolites Y consist exclusively of signals of the tetrahedrally coordinated framework aluminum atoms with spectroscopic parameters similar to those of framework aluminum atoms in hydrated samples. The framework n_Si/n_Al ratios of the non-hydrated zeolites Y obtained by both ²⁹Si and ²⁷Al MAS NMR spectroscopy upon ammonia-loading agree well with each other.     

Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems

Dynamic nuclear polarization (DNP) has shown great promise as a tool to enhance the nuclear magnetic resonance signals of proteins in the cellular environment. As sensitivity increases, the ability to select and efficiently polarize a specific macromolecule over the cellular background has become desirable. Herein, we address this need and present a tetrazine-based DNP agent that can be targeted selectively to proteins containing the unnatural amino acid (UAA) norbornene-lysine. This UAA can be introduced efficiently into the cellular milieu by genetic means. Our approach is bio-orthogonal and easily adaptable to any protein of interest. We illustrate the scope of our methodology and investigate the DNP transfer mechanisms in several biological systems. Our results shed light on the complex polarization-transfer pathways in targeted DNP and ultimately pave the way to selective DNP-enhanced NMR spectroscopy in both bacterial and mammalian cells.     

Heparin Modulates the Mitogenic Activity of Fibroblast Growth Factor by Inducing Dimerization of its Receptor. A 3D View by Using NMR

In vitro mitogenesis assays have shown that sulfated glycosaminoglycans (GAGs; heparin and heparan sulfate) cause an enhancement of the mitogenic activity of fibroblast growth factors (FGFs). Herein, we report that the simultaneous presence of FGF and the GAG is not an essential requisite for this event to take place. Indeed, preincubation with heparin (just before FGF addition) of cells lacking heparan sulfate produced an enhancing effect equivalent to that observed when the GAG and the protein are simultaneously added. A first structural characterization of this effect by analytical ultracentrifugation of a soluble preparation of the heparin‐binding domain of fibroblast growth factor receptor 2 (FGFR2) and a low molecular weight (3 kDa) heparin showed that the GAG induces dimerization of FGFR2. To derive a high resolution structural picture of this molecular recognition process, the interactions of a soluble heparin‐binding domain of FGFR2 with two different homogeneous, synthetic, and mitogenically active sulfated GAGs were analyzed by NMR spectroscopy. These studies, assisted by docking protocols and molecular dynamics simulations, have demonstrated that the interactions of these GAGs with the soluble heparin‐binding domain of FGFR induces formation of an FGFR dimer; its architecture is equivalent to that in one of the two distinct crystallographic structures of FGFR in complex with both heparin and FGF1. This preformation of the FGFR dimer (with similar topology to that of the signaling complex) should favor incorporation of the FGF component to form the final assemblage of the signaling complex, without major entropy penalty. This cascade of events is probably at the heart of the observed activating effect of heparin in FGF‐driven mitogenesis.     

Characterization of unsaturated polyester and alkyd resins using one‐ and two‐dimensional NMR spectroscopy

One‐ (1D) and two‐dimensional (2D) ¹H‐ and ¹³C‐NMR spectroscopy was used to characterize polyester and alkyd resins used in the coatings industry. The wealth of chemical composition information of the ¹H‐ and ¹³C‐NMR 1D spectra of the resins is revealed through 2D NMR experiments that spread chemical shifts in two dimensions, thus facilitating the peak assignment of the various components of the resins. It is shown that the types of polyols, acids, and vegetable oils used to modify the resins can be efficiently traced by NMR spectroscopic techniques. Information on the quantitative composition of the resins and especially the abundance of unsaturated fatty acid double bonds, which influences resin dryability and hardness, can be easily extracted from the ¹H‐NMR spectra upon successful assignment. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 1881–1888, 2003     

Drug Screening Boosted by Hyperpolarized Long‐Lived States in NMR

Transverse and longitudinal relaxation times (T_1ρ and T₁) have been widely exploited in NMR to probe the binding of ligands and putative drugs to target proteins. We have shown recently that long‐lived states (LLS) can be more sensitive to ligand binding. LLS can be excited if the ligand comprises at least two coupled spins. Herein we broaden the scope of ligand screening by LLS to arbitrary ligands by covalent attachment of a functional group, which comprises a pair of coupled protons that are isolated from neighboring magnetic nuclei. The resulting functionalized ligands have longitudinal relaxation times T₁(¹H) that are sufficiently long to allow the powerful combination of LLS with dissolution dynamic nuclear polarization (D‐DNP). Hyperpolarized weak “spy ligands” can be displaced by high‐affinity competitors. Hyperpolarized LLS allow one to decrease both protein and ligand concentrations to micromolar levels and to significantly increase sample throughput.     

An in vitro Assay to Measure Targeted Drug Delivery to Bone Mineral

Targeted delivery of drugs to their site of action is a promising strategy to decrease adverse effects and enhance efficacy, but successful applications of this strategy have been scarce. Human bone is a tissue with unique properties due to its high hydroxyapatite mineral content. However, with the exception of bisphosphonates, bone mineral has not been targeted in a successful clinical application of drugs that act on bone, such as anti‐resorptive or bone anabolic agents. Herein we present an NMR‐based in vitro assay to measure binding affinities of small molecules to hydroxyapatite (HAP) or bone powder. Binding was shown to be specific and competitive, and the assay can be carried out in a direct binding format or in competition mode. A selection of clinically relevant bisphosphonates was ranked by their binding affinity for HAP. The binding affinity decreases in the order: pamidronate > alendronate > zoledronate > risedronate > ibandronate. The differences in binding affinities span a factor of 2.1 between pamidronate and ibandronate, consistent with previous studies. The rank order is very similar with bone powder, although the binding capacity of bone powder is smaller and binding kinetics are slower. A zoledronate derivative that lacks the central hydroxy group binds to HAP with 2.3‐fold weaker affinity than zoledronate itself. Any small molecule can be analyzed for its binding to HAP or bone powder, and the binding of common bone‐staining agents such as alizarin and its derivatives was confirmed in the new assay. This assay supports a strategy for targeted delivery of drugs to bone by attaching a bone‐affinity tag to the active drug substance.     

Practical nuclear magnetic resonance analysis of liquid oil in oilseeds: I factors affecting peak width

If proton nuclear magnetic resonance (NMR) spectra of single seeds can be improved, a rapid, low-cost method of screening seeds for oil composition could be developed for use as a selection tool in plant breeding. NMR spectroscopy was performed on single seeds of borage, flax, and canola to evaluate methods for improving spectra quality (narrowing peak widths and increasing signal-to-noise ratio) to a degree necessary to measure differences among seeds in a breeding program. Immersion of seeds in a variety of solvents, including deuterated chloroform, deuterated acetone, deuterated dimethyl sulfoxide (DMSO) and completely fluorinated hydrocarbons (FC-77), narrowed peaks obtained from seeds when compared with spectra from seeds analyzed in the absence of a solvent. Deuterated chloroform and FC-77 were free of interfering solvent proton peaks while deuterated acetone and deuterated DMSO contributed interfering peaks. The spectra of dehulled seeds had narrower peak widths than did seeds with hulls. Treatments that decreased seed oil viscosity failed to substantially narrow spectra peak widths of seeds. High magnetic field strength did not improve the spectral quality of seeds, as peak widths increased with field strength. Conversely, low field strength limited resolution of oil spectra. Although the 300 MHz spectrum of vegetable oil had greater resolution (narrower peaks) than the 60 MHz spectrum, spectra of seeds produced at 60 MHz had superior resolution to 300 MHz spectra.     

Characterization of poly(1‐methyl‐1,4‐butanediol‐1,4‐diyl/2,3,4‐trihydro‐5‐methylfuran‐2,5‐diyl) prepared from natural rubber through 2D NMR spectroscopy

Poly(1‐methyl‐1,4‐butanediol‐1,4‐diyl/2,3,4‐trihydro‐5‐methylfuran‐2,5‐diyl) was prepared by epoxidation of deproteinized natural rubber with m‐chloroperbenzoic acid followed by hydrolysis with sulfuric acid. Characterization of the resulting product was performed through FT‐IR, ¹H NMR, and ¹³C NMR spectroscopies. All signals appearing in the ¹H and ¹³C NMR spectra were assigned by distortionless enhancement by polarization transfer (DEPT), quaternary carbon observation (QUAT), correlation spectroscopy (COSY), and heteronuclear multiple quantum correlation (HMQC) measurements. After proving the primary structure of the product, one pot synthesis of poly(1‐methyl‐1,4‐butanediol‐1,4‐diyl/2,3,4‐trihydro‐5‐methylfuran‐2,5‐diyl) from deproteinized natural rubber latex was carried out with peracetic acid and 2‐propanol. The resulting product was characterized by ¹H NMR spectroscopy on the basis of the assignments established in this study, and its gas permeability was measured for a practical application as a film. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011.     

1H‐ and 13C‐NMR analyses of aqueous polyamideamine–epichlorohydrin resin solutions

More accurate signal assignment for ¹H‐ and ¹³C‐NMR spectra of aqueous solutions of polyamideamine‐epichlorohydrin (PAE) resin and its related compounds was achieved by using distortionless enhancement of polarization transfer (DEPT) and C‐H correlation spectroscopy (COSY) methods. On the basis of the assignment, we developed new methods to determine the content of four‐membered azetidinium ring (AZR) and number‐average degree of polymerization (DP_n) of the repeating unit of PAE by using NMR. Degree of introduction of epichlorohydrin into polyamideamine chains at the initial stage was 75–80%, and the resultant AZR content per one repeating unit in the PAE sample prepared in this study was about 72%. DP_n of the initial polyamideamine was 32, and this value decreased to about 18 during the PAE preparation process. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 1847–1854, 2004     

Nuclear magnetic resonance studies of N‐vinylcarbazole/methyl methacrylate copolymers

Copolymers of N‐vinylcarbazole and methyl methacrylate of different compositions were prepared by solution polymerization with azobisisobutyronitrile as an initiator, and their compositions were determined from quantitative ¹³C{¹H}‐NMR spectroscopy. The reactivity ratios for the comonomers were calculated with the Kelen–Tudos and nonlinear error‐in‐variable methods. The complete spectral assignment of the overlapping ¹H and ¹³C{¹H} spectra of the copolymers was made with the help of distortionless enhancement by polarization transfer, two‐dimensional heteronuclear single‐quantum correlation, and total correlation spectroscopy. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 3005–3012, 2003     

Structural and Functional Analysis of Human Liver‐Expressed Antimicrobial Peptide 2

Human liver‐expressed antimicrobial peptide 2 (LEAP‐2) is a cationic antimicrobial peptide (CAMP) believed to have a protective role against bacterial infection. Little is known about the structure–activity relationships of LEAP‐2 or its mechanism of action. In this study we describe the structure of LEAP‐2, analyze its interaction with model membranes, and relate them to the antimicrobial activity of the peptide. The structure of LEAP‐2, determined by NMR spectroscopy, reveals a compact central core with disorder at the N and C termini. The core comprises a β‐hairpin and a 3₁₀‐ helix that are braced by disulfide bonds between Cys17–28 and Cys23–33 and further stabilized by a network of hydrogen bonds. Membrane‐affinity studies show that LEAP‐2 membrane binding is governed by electrostatic attractions, which are sensitive to ionic strength. Truncation studies show that the C‐terminal region of LEAP‐2 is irrelevant for membrane binding, whereas the N‐terminal (hydrophobic domain) and core regions (cationic domain) are essential. Bacterial‐growth‐inhibition assays reveal that the antimicrobial activity of LEAP‐2 correlates with membrane affinity. Interestingly, the native and reduced forms of LEAP‐2 have similar membrane affinity and antimicrobial activities; this suggests that disulfide bonds are not essential for the bactericidal activity. This study reveals that LEAP‐2 has a novel fold for a CAMP and suggests that although LEAP‐2 exhibits antimicrobial activity under low‐salt conditions, there is likely to be another physiological role for the peptide.     

Schiff base polymers derived from 2,5‐diformylfuran

Polymerization of 2,5‐diformylfuran with two primary amines was carried out in acetonitrile and ethanol at room temperature. The reaction was characterized using a combination of mass spectroscopy and NMR spectroscopy, which revealed the clean formation of the imine –CH?N? functional group. Although some cyclic products were detected from mass spectroscopy, the ring size was limited to products that have the ?CH?N? group only in anti‐geometry. The furan Schiff bases exhibit good thermal stability. While mass spectra evidenced oligomers of different lengths, cross‐polarization magic angle spinning ¹³C NMR spectra of the insoluble polymer revealed the linear structure as proposed. © 2013 Society of Chemical Industry     

六烯丙基六氮杂异伍兹烷的核磁表征

为精确表征六烯丙基六氮杂异伍兹烷(HAIW)的化学结构,在氘代氯仿(CDCl3)及氘代丙酮(acetone-d6)中研究了HAIW的核磁谱图特征。采用一维及二维1 H、13 C、15 N NMR技术对HAIW的NMR信号进行了全归属,利用核磁模拟软件NMR-SIM对氢谱图进行计算机拟合。结果表明,HAIW在丙酮溶液中的1 H NMR的分辨率较好,谱图中存在两类异伍兹烷信号(环内与桥头)及两类烯丙基碳氢信号,其中五元环所连4个烯丙基不能自由旋转导致亚甲基氢不对称出现2组峰,而六元环所连2个烯丙基则能自由旋转使得该亚甲基氢对称重合;两类烯丙基存在的多种偶合使得氢谱谱线较为复杂;由拟合氢谱化学位移及偶合常数获得的1 H NMR谱图与实际图谱完全一致。表明二维核磁共振技术与核磁模拟技术相结合,可用于对复杂谱的精确分析。     

Preparation and characterization of thermoplastic polyurethane–urea and carboxylated acrylonitrile butadiene rubber blend nanocomposites

This study deals with the preparation and characterization of novel thermoplastic polyurethane–urea (TPUU) and carboxylated acrylonitrile butadiene rubber (XNBR) blends. Blends of different compositions were prepared in tetrahydrofuran using a solution technique, following an ultra‐sonication. The chemical reaction between the two inherently immiscible blend phases was determined with the help of Fourier transform infrared‐attenuated total reflectance (FTIR‐ATR) spectroscopy and ¹H‐nuclear magnetic resonance (¹H‐NMR) spectroscopy. The identification of the new peaks in the FTIR‐ATR spectra corroborates the existence of chemical reaction between the carboxylic functional group of XNBR and the amide group of the TPUU. In addition, an increase in the network crosslink density of the blend investigated using ¹H‐NMR spectroscopy further supports the occurrence of the chemical reaction between the XNBR and the TPUU. The scanning and transmission electron micrographs of the blend morphology show a uniform dispersion of the minor TPUU phase in the XNBR. Furthermore, the existence of a single glass transition peak also confirms the enhancement in the interfacial miscibility. Additionally, the incorporation of 5 wt % of organomodified montmorillonite nanoclay improves the mechanical properties to a considerable extent in comparison with the unfilled blend elastomeric material. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012     

Protein NMR Spectroscopy at 150 kHz Magic-Angle Spinning Continues To Improve Resolution and Mass Sensitivity

Spectral resolution is the key to unleashing the structural and dynamic information contained in NMR spectra. Fast magic-angle spinning (MAS) has recently revolutionized the spectroscopy of biomolecular solids. Herein, we report a further remarkable improvement in the resolution of the spectra of four fully protonated proteins and a small drug molecule by pushing the MAS rotation frequency higher (150 kHz) than the more routinely used 100 kHz. We observed a reduction in the average homogeneous linewidth by a factor of 1.5 and a decrease in the observed linewidth by a factor 1.25. We conclude that even faster MAS is highly attractive and increases mass sensitivity at a moderate price in overall sensitivity.