NMR spectroscopy of RNA

NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.     

NMR spectroscopy as basis for characterization of Pluronic® F108 and its derivatives

The hydroxyl end groups of Pluronic®F108 {a triblock copolymer surfactant of poly(ethylene glycol) and poly(propylene glycol) [PEG‐PPG‐PEG]} were modified into primary amine, sulfonic acid, and quaternary ammonium equivalents for use in affinity chromatography. NMR was used for monitoring the efficacy of modifications on intermediaries and final products. The primary amine equivalents were prepared via conversion of the hydroxyl groups to a tosylate, its displacement with an azide, followed by reduction to the primary amine. The sulfonic acid equivalents were prepared via hydroxyl group tosylation, the displacement of tosylate with thiol, and its oxidation to sulfonic acid. The conversion to trimethyl ammonium was achieved via hydroxyl group tosylation, tosylate displacement by halide, and halide displacement with trimethylamine. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 109–117, 2000     

Structural characterization of maleic anhydride grafted polyethylene by C NMR spectroscopy

Maleic anhydride grafted polyethylene, [2,3-¹³C₂] MA-g-PE, which was synthesized with ¹³C labeled maleic anhydride [2,3-¹³C₂] MA in solution, was characterized by ¹³C NMR spectroscopy in order to make clear the structure of graft groups. The results reveal that [2,3-¹³C₂] MA-g-PE has succinic anhydride oligomeric grafts with a terminal unsaturated MA ring in addition to well-known saturated succinic anhydride oligomeric grafts and that the former grafts are longer but fewer than the latter.     

Structural characterization of FCC feeds from Indian refineries by NMR spectroscopy

Fluid catalytic cracking (FCC) feeds from four Indian refineries are structurally characterized by ¹H, gated-decoupled ¹³C, distortionless enhancement by polarization transfer (DEPT) and 2D ¹H–¹³C HETeronuclear CORrelation (HETCOR) and other 2D nuclear magnetic resonance (NMR) methods. Detailed structural analyses are completely supported by a range of NMR information including chemical shifts of ¹H and ¹³C, CH_n type distributions and ¹H –¹³C connectivities. The average structural parameters like branching sites, average number of branching per molecule, average length of side chains, percentage of saturates, aromatics and naphthenes are obtained from these NMR data. A novel approach based on “multipoint spline base line correction” is employed for estimation of naphthenes and n-paraffins that gives better quantitative estimation than the conventional methods. In this paper, importance is given to the study of those structural parameters that plays a key role in cracking chemistry as well as coke forming tendency of the feedstock. To the best of our knowledge, this is the first attempt to characterize and quantitatively estimate compositions of the high boiling fractions of petroleum feed by NMR methods and especially the complex structure of vacuum gas oil (VGO) fractions used in Indian refineries. The importance of this paper is to help in optimizing the product slate of Indian refineries through proper feedstock blending using few hundreds of million metric tons (MMT) of crude oil consisting of blends of light crudes with different heavy crudes and bottom of the barrel due to escalating cost of crudes.     

Monomer sequence characterization of propylene-1-olefin copolymers by carbon-13 NMR spectroscopy

Complete comonomer sequence assignments were made for a series of propylene-1-olefin copolymers, including 1-butene, 1-hexene, and 1-octene, to establish the effect of branch length on the sequence sensitivity of the backbone carbon chemical shifts. Particular attention was paid to the effect of branch length on the monomer sequence sensitivity of the αα carbon chemical shifts. As opposed to the ethylene-1-olefin copolymers where the reported αα carbon chemical shifts were exclusively tetrad sensitive regardless of the branch length, the αα carbons in each of the three propylene-1-olefin systems examined showed apparent tetrad, triad, and dyad monomer sequence sensitivities as the center dyad changed from PP to PX to XX where X represents the individual 1-olefin.     

Stabilizer insights by NMR spectroscopy

During the past decade, advances in both hardware and software have made NMR spectroscopy an enormously powerful analytical technique. In this paper, the author presents examples of the use of NMR in support of vinyl stabilizer research; he also covers representative practical applications of proton, carbon, phosphorus, and tin NMR.     

RNA Dynamics by NMR Spectroscopy

An ever-increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined—Lego like—than in proteins, hence the numerous revelations of RNA excited states.     

High resolution NMR spectroscopy and some examples of its use

High resolution nuclear magnetic resonance (NMR) spectroscopy has gained wide acceptance in the study of fatty acids and other lipids. Some of the techniques are described and examples of identification and structure determination of fatty compounds are given. Nuclear magnetic resonance spectroscopy is of particular value in the examination of acids with various types of unsaturation, such as mono- and polyenoic, acetylenic, allenic and conjugated. Acids with a cyclopropene or cyclopropane ring have been detected and studied by NMR. Positional isomers of certain substituted acids can be identified by the NMR spectrum alone. Other lipids such as glyceryl ethers, phosphatidylcholines, sphingomyelin and plasmalogens have been investigated with the aid of NMR. Reference is made to studies of other compounds, including steroids, rotenones, gossypol, glycosides, sugars, amines, amino acids and polymers. Issued as N.R.C. No. 10440. Presented at the AOCS-AACC Joint Meeting, Washington, D.C., April, 1968.     

Authentication of marine oils using 13C NMR spectroscopy

NMR spectroscopy has been particularly valuable in the study of lipids, since it provides qualititative and quantitative information on chemically diverse compounds in a non‐destructive and non‐selective fashion. NMR gives a fingerprint of the sample analyzed and may be used as a rapid profiling technique. Combined with chemometrics and databases with relevant authentic samples, ¹³C NMR is a powerful tool for authentication of marine oils.     

NMR characterization of dihydrosterculic acid and its methyl ester

Cyclopropane FA occur in nature in the phosphoplipids of bacterial membranes, in oils containing cyclopropene FA, and in Litchi sinensis oil. Dihydrosterculic acid (2-octyl cyclopropaneoctanoic acid) and its methyl ester were selected for ¹H and ¹³C NMR analysis as compounds representative of cyclopropane FA. The 500 MHz ¹H NMR spectra acquired with CDCl₃ as solvent show two individual peaks at −0.30 and 0.60 ppm for the methylene protons of the cyclopropane ring. Assignments were made with the aid of 2D correlations. In accordance with previous literature, the upfield signal is assigned to the cis proton and the downfield signal to the trans proton. This signal of the trans proton is resolved from the peak of the two methine protons of the cyclopropane ring, which is located at 0.68 ppm. The four protons attached to the two methylene carbons α to the cyclopropane ring also show a split signal. Two of these protons, one from each methylene moiety, display a distinct shift at 1.17 ppm, and the signal of the other two protons is observed at 1.40 ppm, within the broad methylene peak. The characteristic peaks in the ¹³C spectra are also assigned.     

Structural characterization of nylon 4 in the solid state by high-resolution solid-state H NMR spectroscopy

High-resolution solid-state ¹H NMR spectra of nylon 4 melt-quenched sample and single crystal sample in the solid state were measured in a wide range of temperatures from room temperature to 505 K by using solid state 300 MHz NMR with the FSLG-2 homo-nuclear dipolar decoupling method combined with high speed magic angle spinning method. From the experimental results, structural characterization on the crystalline and non-crystalline components was carried out. Further, intermolecular interaction between nylon 4 and water contained in the sample was discussed.     

Nano-particles seeding and its characterization by X-ray photoelectron spectroscopy (XPS)

We present a new procedure for pretreatment seeding by ultrasonic agitation of silicon substrates in diamond nano-powder suspensions to which HF and KOH were added X-ray photoelectron spectroscopy (XPS) was used to measure the surface coverage by diamond nuclei immediately after the pretreatment. Coverage percentages of 70, 40 and 55% were obtained for the HF, KOH and the original diamond slurry, respectively. The seeding density (S_D) was calculated from the known nano-particles size, determined independently from X-ray diffraction of the powder. For nano-particle size of ∼6 nm, we obtain nominal seeding densities of the order ∼10¹² cm⁻². The advantage of the high coverage was most evident for films deposited at low substrate temperature (570 °C). The potential of the new seeding procedure and the XPS characterization method are discussed.     

Application of NMR spectroscopy to the characterization of elastomer/filler interactions

Proton spin–spin relaxation time measurements have been performed at 300 and 400 MHz on bound rubber-filler mixes resulting from the solvent extraction of silica-filled and silicafilled-modified polybutadiene, on the one hand, and of carbon black-filled and carbon blackfilled-modified styrene butadiene rubber, on the other hand. Two relaxation times are observed for all samples. They are ascribed to the occurrence of tightly and loosely bound rubber components, respectively. The effect of the grafting modification of the fillers on the formation of bound rubber and its two components is discussed. © 1992 John Wiley & Sons, Inc.     

TEABr directed synthesis of ZSM-12 and its NMR characterization

Synthesis of ZSM-12 using tetraethylammonium bromide (TEABr) as the template was investigated. Among the various parameters that affect the crystallization of ZSM-12, aluminum content of the gel, OH⁻/SiO₂ and TEA/SiO₂ ratios were the important determinants. Systematic variations of these parameters revealed that the TEABr-assisted synthesis had many similarities to the synthesis using TEAOH template reported earlier, with the exception that the OH⁻/SiO₂ ratios had to be maintained at lower values. Furthermore, the OH⁻/SiO₂ ratios favorable for ZSM-12 formation lie in a very narrow range. The source of alkalinity also affected the rate of crystallization and the composition of the product. The crystallization was found to be faster and better incorporation of aluminum in the zeolite framework was obtained when NaOH was used to provide alkalinity rather than KOH. Successful synthesis of highly crystalline ZSM-12 samples with Si/Al ratio around 30 was achieved using a minimal amount of relatively inexpensive TEABr (TEA/SiO₂=0.125).

Aluminum-27 NMR spectroscopy unambiguously revealed that all aluminum atoms are incorporated in the zeolite framework in tetrahedral coordination. The NMR line-widths of aluminum signals of the calcined samples were significantly larger than those with template incorporated samples. Spin-lattice relaxation times, conventional and rotating frame, as well as magic angle spinning (MAS) cross-polarization data with variable contact time support that there is a significant proton reservoir in the aluminum framework. The NMR data indicate that many distorted tetrahedral sites are formed upon removal of the template and some of these sites contain Al–OH moieties.     

Gasoline composition determined by H NMR spectroscopy

A fast and simple ¹H NMR spectroscopic method was developed for the concentration measurement of aromatic, olefinic and aliphatic fractions in gasoline samples. Simultaneously, individual components such as benzene, methyl tert-butyl ether and several dienes could be determined. The method relies on only a few, well-established assumptions about the molecular compositions and is therefore applicable to a broad range of gasolines. It is well suited for laboratories with high sample throughput since measurement time is short and all concentrations are determined within one NMR experiment. The method was applied to commercial gasolines and samples used in European round robin tests. Comparisons of NMR and round robin test results showed excellent agreement.     

Characterization by solid state V NMR spectroscopy

The fresh catalyst V₂O₅–WO₃/TiO₂ and catalyst used in SCR for 9000 h have been studied by the solid state ⁵¹V NMR spectroscopy in static and MAS conditions. According to ⁵¹V NMR in both samples the majority of vanadium sites are in a distorted octahedral environment similar to that in V₂O₅. There is a strong interaction between vanadium oxide and the support, but the concentration of vanadium atoms strongly bound to the surface is very small and can be detected only in MAS NMR experiments or after removing the excess of V₂O₅. There is no influence of WO₃ additives on the structure of the particles of V₂O₅, whereas the influence on the structure of strongly bounded V cannot be excluded. Combination of static (wide line) and MAS NMR techniques permit the characterization of not only the structure of the vanadium species but also small changes in their local environment. Hence these experiments show that there are some distortions of the local environment of vanadium sites of the vanadium oxide particles compared with the polycrystalline V₂O₅; treatment by SCR increases these distortions.     

What function for human lithostathine?: structural investigations by three-dimensional structure modeling and high-resolution NMR spectroscopy

Human lithostathine is a 144-residue protein, expressed in variousorgans and pathologies. Several biological functions have beenproposed for this protein. Among others, inhibition of nucleationand growth of CaCO₃ crystals in the pancreas and bacterial aggregationhas retained attention, because lithostathine presents highsequence similarities with calcium-dependent (or C-type) lectins.To study its structure-function relationship and compare itwith that of C-type lectins, we have built a model for lithostathine.This model is derived from the only two C-type lectins of knownstructures: rat mannose binding protein and human E-selectin.An original strategy, inspired by that proposed by Havel andSnow, was designed for model building. We have undertaken NMRstudies on the natural protein. Although complete structuredetermination has not yet been achieved, the NMR studies didconfirm the main characteristics of the model. From analysisof the proposed model, we concluded that lithostathine is notexpected to present sugar- or calcium-binding properties. Therefore,the mechanisms of bacterial aggregation and inhibition of CaCO₃nucleation and growth have not yet been elucidated.