Nuclear Overhauser effects determination

Another technique often used to examine the stmcture of double-heUcal oligonucleotides is two-dimensional nmr spectroscopy (see AfAGNETiC SPIN resonance). This method rehes on measurement of the nuclear Overhauser effects (NOEs) through space to determine the distances between protons (6). The stmcture of an oligonucleotide may be determined theoretically from a set of iaterproton distances. As a result of the complexities of the experiment and data analysis, the quality of the stmctural information obtained is debated. However, nmr spectroscopy does provide information pertaining to the stmcture of DNA ia solution and can serve as a complement to the stmctural information provided by crystallographic analysis. 

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

Keepers, J.W. and James, T.L., A theoretical smdy of distance determinations from NMR two-dimensional nuclear Overhauser effect spectra, J. Mag. Resort, 57, 404, 1984. Kemp, W., Organic Spectroscopy, 3rd ed., W.H. Ereeman, New York, 1991. Figueiredo, P. et al., New aspects of anthocyanin complexation intramolecular copigmentation as a means for colour loss Phytochemistry, 41, 301, 1996. 

The relative stereochemistry of hyperaspine 93 was determined by 2-D NMR spectroscopic and mass spectrometry (MS) methods. It has a m-fused bicyclic conformation 93a <2001TL4621>. The trans-fused one is disfavored by an axial pentyl group at C-8 and by a destabilizing dipole-dipole interaction between the N- and O-atoms, which does not exist in the alternative //.(-conformation. The geminal coupling constant of C( 1 )H2 in 93 (11.0 Hz), and that of its 6-hydroxy derivative (11.2 Hz), indicates that they exist preferentially in / //-conformations, whereas their 6-epimers adopt trans-conformations (9.3 and 8.4 Hz, respectively) <2005EJ01378>. Nuclear Overhauser enhancement spectroscopy (NOESY) studies also confirmed the stereochemistry of 93 by the marked nuclear Overhauser effect (NOE) correlation between H-3 and H-4a <20030L5063>. 

Benzoylation of D-g/ycero-D-gw/o-heptono-1,4-lactone with an excess of benzoyl chloride and pyridine afforded the hept-2-enono-1,4-lactone as the main product (198). The di- and triunsaturated compounds were isolated in very low yield from the mother liquors (199). Higher yields of the di- and triunsaturated derivatives 153 and 154 were obtained when the /5-elimination reaction was performed with triethylamine on the previously synthesized per-O-benzoyl D-g/ycero-D-gw/o-heptono-1,4-lactone. Employing 10% triethylamine in chloroform, the lactone 153 was obtained as an E, Z dias-tereomeric mixture in 9 11 ratio as determined by H n.m.r. When 20% triethylamine was used, the furanone 154 was obtained in 59% yield (200). Its structure was assigned, on the basis of H and 13C n.m.r. spectra, as 3 -benzoyloxy - (5Z)-[(Z)-3 - benzoyloxy - 2 - propenyliden] -2(5 H)- furanone. The stereochemistry of the exocyclic double bonds was established (201) by nuclear Overhauser effect spectroscopy (NOESY). 

The principle source of experimental conformational data in an NMR structure determination is constraints on short interatomic distances between hydrogen atoms obtained from NMR measurements of the nuclear Overhauser effect (NOE). NOEs result from cross-relaxation mediated by the dipole-dipole interaction between spatially proximate nu-... 

In de novo three-dimensional structure determinations of proteins in solution by NMR spectroscopy, the key conformational data are upper distance limits derived from nuclear Overhauser effects (NOEs) [11, 14]. In order to extract distance constraints from a NOESY spectrum, its cross peaks have to be assigned, i.e. the pairs of hydrogen atoms that give rise to cross peaks have to be identified. The basis for the NOESY assignment... 

Sowinski and coworkers40 reported a structure of vacidin A (63), an aromatic hep-taene macrolide antibiotic. The constitution of vacidin A, a representative of the aromatic heptaene macrolide antibiotics, was established on the basis of 13C and H- H double quantum filtered correlated spectroscopy, rotating frame nuclear Overhauser effect spectroscopy, 7-resolved 11 as well as H-13C correlation NMR spectra. The geometry of the polyene chromophore was determined as 22E, 24E, 26E, 28Z, 30Z, 32E, 34E. 

The rotational relaxation time zK can be combined with time-dependent nuclear Overhauser effect (NOE) measurements to determine interproton... 

TTie TOCSY 2D NMR experiment correlates all protons of a spin system, not just those directly connected via three chemical bonds. For the protein example, the alpha proton, Ft , and all the other protons are able to transfer magnetization to the beta, gamma, delta, and epsilon protons if they are connected by a continuous chain—that is, the continuous chain of protons in the side chains of the individual amino acids making up the protein. The COSY and TOCSY experiments are used to build so-called spin systems—that is, a list of resonances of the chemical shift of the peptide main chain proton, the alpha proton(s), and all other protons from each aa side chain. Which chemical shifts correspond to which nuclei in the spin system is determined by the conventional correlation spectroscopy connectivities and the fact that different types of protons have characteristic chemical shifts. To connect the different spin systems in a sequential order, the nuclear Overhauser effect spectroscopy... 

Hence, provided that I g is known and that R has been determined by means of an independent experiment, provides the cross-relaxation rate ct. This enhancement is called nuclear Overhauser effect (nOe) (17,19) from Overhauser (20) who was the first to recognize that, by a related method, electron spin polarization could be transferred to nuclear spins (such a method can be worked out whenever EPR lines are relatively sharp it is presently known as DNP for Dynamic Nuclear Polarization). This effect is usually quantified by the so-called nOe factor p... 

No such chemical exchange is observed for NP2—ImH or NP3—ImH, for which WEFT-NOESY spectra have cross peaks due only to through-space nuclear Overhauser effect interactions (91). Interestingly, these two proteins have only one proline in the A-B loop (Fig. 4). However, considerable additional NMR investigation needs to be carried out in order to determine whether the chemical exchange process shown in the NOESY spectra of NPl-ImH is indeed due to the dynamics of the A-Bloop. 

The basis for the determination of solution conformation from NMR data lies in the determination of cross relaxation rates between pairs of protons from cross peak intensities in two-dimensional nuclear Overhauser effect (NOE) experiments. In the event that pairs of protons may be assumed to be rigidly fixed in an isotopically tumbling sphere, a simple inverse sixth power relationship between interproton distances and cross relaxation rates permits the accurate determination of distances. Determination of a sufficient number of interproton distance constraints can lead to the unambiguous determination of solution conformation, as illustrated in the early work of Kuntz, et al. (25). While distance geometry algorithms remain the basis of much structural work done today (1-4), other approaches exist. For instance, those we intend to apply here represent NMR constraints as pseudoenergies for use in molecular dynamics or molecular mechanics programs (5-9). 

It is not usually possible to integrate routine C spectra directly unless specific precautions have been taken. However with proper controls, NMR spectroscopy can be used quantitatively and it is a valuable technique for the analysis of mixtures. To record C NMR spectra where the relative signal intensity can be reliably determined, the spectra must be recorded with techniques to suppress the Nuclear Overhauser Effect and with a long delay between the acquisition of successive spectra to ensure that all of the carbons in the molecule are completely relaxed between spectral acquisitions. 

Nuclear Overhauser effect—The nuclear Overhauser effect (NOE) occurs only between nuclei that share a dipole coupling, i.e., their nuclei are so close that their magnetic dipoles interact. Techniques that use NOE enhance spectra and allow spacial relationships of protons to be determined. 

Two-Dimensional NMR—Basically, the two-dimensional NMR techniques of nuclear Overhauser effect spectroscopy (NOESY) and correlation spectroscopy (COSY) depend on the observation that spins on different protons interact with one another. Protons that are attached to adjacent atoms can be directly spin-coupled and thus can be studied using the COSY method. This technique allows assignment of certain NMR frequencies by tracking from one atom to another. The NOESY approach is based on the observation that two protons closer than about 0.5 nm perturb one another s spins even if they are not closely coupled in the primary structure. This allows spacial geometry to be determined for certain molecules. 

The isotope N, with a natural abundance of 99.9%, has nuclear spin 7 = 1 and gives broad signals which are of little use for structural determinations. The N nucleus, with I = 1/2, is therefore preferred. However, the low natural abundance of about 0.4% and the extremely low relative sensitivity (Table 1) make measurements so difficult that N NMR spectroscopy was slow to become an accepted analytical tool. A further peculiarity is the negative magnetogyric ratio since, in proton decoupled spectra, the nuclear Overhauser effect can strongly reduce the signal intensity. DEPT and INEPT pulse techniques are therefore particularly important for N NMR spectroscopy. 

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