Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics

Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The H-1 resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T-12 and U-15 nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T-14 stacks upon both T-12 and U-15 while T-13 partially stacks upon T-14. Very weak stacking interaction is observed between T-13 and T-12. All the individual nucleotide bases adopt 'anti' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T-13 and T-14. The stereochemistry of U-15 mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.

NMR methods for fast data acquisition

NMR spectroscopy has witnessed tremendous advancements in recent years with the development of new methodologies for structure determination and availability of high-field strength spectrometers equipped with cryogenic probes. Supported by these advancements, a new dimension in NMR research has emerged which aims to increase the speed with data is collected and analyzed. Several novel methodologies have been proposed in this direction. This review focuses on the principles on which these different approaches are based with an emphasis on G-matrix Fourier transform NMR spectroscopy.

Intra-molecular hydrogen bonding with organic fluorine in the solution state: Deriving evidence by a two dimensional NMR experiment

The direct evidence for the existence of intra-molecular C-F center dot center dot center dot H-N hydrogen bond in organofluorine molecules, in the liquid state, is derived using NMR spectroscopy by the detection of long range interactions among fluorine, nitrogen and hydrogen atoms. The present study reports the determination of the relative signs and magnitudes of through space and through bond couplings to draw unambiguous evidence on the existence of weak molecular interactions involving organic fluorine. It is a simple, easy to implement, N-15 natural abundant two dimensional heteronuclear N-15-H-1 double quantum-single quantum correlation experiment. The existence of intra-molecular hydrogen bond is conclusively established in the investigated molecules. (C) 2011 Elsevier B.V. All rights reserved.

NMR studies of preimplantation embryo metabolism in human assisted reproductive techniques: a new biomarker for assessment of embryo implantation potential

There has been growing interest in understanding energy metabolism in human embryos generated using assisted reproductive techniques (ART) for improving the overall success rate of the method. Using NMR spectroscopy as a noninvasive tool, we studied human embryo metabolism to identify specific biomarkers to assess the quality of embryos for their implantation potential. The study was based on estimation of pyruvate, lactate and alanine levels in the growth medium, ISM1, used in the culture of embryos. An NMR study involving 127 embryos from 48 couples revealed that embryos transferred on Day 3 (after 72 h in vitro culture) with successful implantation (pregnancy) exhibited significantly (p < 10(-5)) lower pyruvate/alanine ratios compared to those that failed to implant. Lactate levels in media were similar for all embryos. This implies that in addition to lactate production, successfully implanted embryos use pyruvate to produce alanine and other cellular functions. While pyruvate and alanine individually have been used as biomarkers, the present study highlights the potential of combining them to provide a single parameter that correlates strongly with implantation potential. Copyright (C) 2012 John Wiley & Sons, Ltd.

``On-the-fly'' kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media

We report the in situ and real-time monitoring of the interconversion of L- and D-alanine-d(3) by alanine racemase from Bacillus stearothermophilus directly observed by H-2 NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their H-2 quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis Menten model.

In situ approach for testing the enantiopurity of chiral amines and amino alcohols by H-1 NMR

An in situ approach involving a simple mix and shake method for testing the enantiopurity of primary, secondary and tertiary chiral amines and their derivatives, chiral amino alcohols, by H-1-NMR spectroscopy is developed. The protocol involves the in situ formation of chiral ammonium borate salt from a mixture of C-2 symmetric chiral BINOL, trialkoxyborane and chiral amines. The proposed concept was demonstrated convincingly on a large number of chiral and pro-chiral amines and amino alcohols, and also aids the precise measurement of enantiomeric excess. The protocol can be completed in a couple of minutes directly in the NMR sample tube, without the need for any physical separation.

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a-p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and beta-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.

Assignment of the C-13 NMR spectrum by correlation to dipolar coupled proton-pairs and estimation of order parameters of a thiophene based liquid crystal

Materials with widely varying molecular topologies and exhibiting liquid crystalline properties have attracted considerable attention in recent years. C-13 NMR spectroscopy is a convenient method for studying such novel systems. In this approach the assignment of the spectrum is the first step which is a non-trivial problem. Towards this end, we propose here a method that enables the carbon skeleton of the different sub-units of the molecule to be traced unambiguously. The proposed method uses a heteronuclear correlation experiment to detect pairs of nearby carbons with attached protons in the liquid crystalline core through correlation of the carbon chemical shifts to the double-quantum coherences of protons generated through the dipolar coupling between them. Supplemented by experiments that identify non-protonated carbons, the method leads to a complete assignment of the spectrum. We initially apply this method for assigning the C-13 spectrum of the liquid crystal 4-n-pentyl-4'-cyanobiphenyl oriented in the magnetic field. We then utilize the method to assign the aromatic carbon signals of a thiophene based liquid crystal thereby enabling the local order-parameters of the molecule to be estimated and the mutual orientation of the different sub-units to be obtained.

Three centered hydrogen bonds of the type C=O...H(N)...X-C in diphenyloxamide derivatives involving halogens and a rotating CF3 group: NMR, QTAIM, NCI and NBO studies

The existence of three centered C=O...H(N)...X-C hydrogen bonds (H-bonds) involving organic fluorine and other halogens in diphenyloxamide derivatives has been explored by NMR spectroscopy and quantum theoretical studies. The three centered H-bond with the participation of a rotating CF3 group and the F...H-N intramolecular hydrogen bonds, a rare observation of its kind in organofluorine compounds, has been detected. It is also unambiguously established by a number of one and two dimensional NMR experiments, such as temperature perturbation, solvent titration, N-15-H-1 HSQC, and F-19-H-1 HOESY, and is also confirmed by theoretical calculations, such as quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) and non-covalent interaction (NCI).

Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) C-13 multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D H-1- H-1] TOCSY and (3) 2D C-13- H-1] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of C-13. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

Study of H/D exchange rates to derive the strength of intramolecular hydrogen bonds in halo substituted organic building blocks: An NMR spectroscopic investigation

Rates of hydrogen/deuterium (H/D) exchange determined by H-1 NMR spectroscopy are utilized to derive the strength of hydrogen bonds and to monitor the electronic effects in the site-specific halogen substituted benzamides and anilines. The theoretical fitting of the time dependent variation of the integral areas of H-1 NMR resonances to the first order decay function permitted the determination of HID exchange rate constants (k) and their precise half-lives (t(1/2)) with high degree of reproducibility. The comparative study also permitted the unambiguous determination of relative strength of hydrogen bonds and the contribution from electronic effects on the HID exchange rate. (C) 2015 Elsevier B.V. All rights reserved.

Self-Assembled Pd(II) Metallocycles Using an Ambidentate Donor and the Study of Square-Triangle Equilibria

The self-assembly reaction of a cis-blocked 90° square planar metal acceptor with a symmetrical linear flexible linker is expected to yield a [4 + 4] self-assembled square, a [3 + 3] assembled triangle, or a mixture of these.However, if the ligand is a nonsymmetrical ambidentate, it is expected to form a complex mixture comprising several linkage isomeric squares and triangles as a result of different connectivities of the ambidentate linker. We report instead that the reaction of a 90° acceptor cis-(dppf)Pd(OTf)2 [where dppf ) 1,1′-bis(diphenylphosphino)- ferrocene] with an equimolar amount of the ambidentate unsymmetrical ligand Na-isonicotinate unexpectedly yields a mixture of symmetrical triangles and squares in the solution. An analogous reaction using cis-(tmen)Pd(NO3)2 instead of cis-(dppf)Pd(OTf)2 also produced a mixture of symmetrical triangles and squares in the solution. In both cases the square was isolated as the sole product in the solid state, which was characterized by a single crystal structure analysis. The equilibrium between the triangle and the square in the solution is governed by the enthalpic and entropic contributions. The former parameter favors the formation of the square due to less strain in the structure whereas the latter one favors the formation of triangles due to the formation of more triangles from the same number of starting linkers. The effects of temperature and concentration on the equilibria have been studied by NMR techniques. This represents the first report on the study of square-triangle equilibria obtained using a nonsymmetric ambidentate linker. Detail NMR spectroscopy along with the ESI-mass spectrometry unambiguously identified the components in the mixture while the X-ray structure analysis determined the solid-state structure.

Unusual Structural Isomerization Of Monopropiophenone Thiocarbonohydrazone

Monopropiophenone thiocarbonohydrazone has been isolated in both linear and cyclic isomeric forms. Each form has been shown to isomerize and exist in equilibrium with the other in DMSO-d6 solution by 1H and 13C NMR spectroscopy. The kinetics of this transformation show attainment of equilibrium in approximately 6 h, with a linear to cyclic configuration ratio of 40:60.

On Coloration of Polyacrylonitrile: A Nuclear Magnetic Resonance Study

Coloration in polyacrylonitrile can be induced in three distinct ways: by heat treatment, by treatment with base, or during synthesis of the polymer itself using ionic initiators at relatively higher temperatures. The present investigation employing 'H and NMR spectroscopy has revealed some common features in colored polyacrylonitrile irrespective of ita mode of coloration. All colored polyacrylonitriles give an additional peak around S 2.7 in 'H NMR spectra and, except for heat-treated polyacrylonitrile, one extra group of peaks in the region 8 12-16 in 13C NMR spectra. The former peak has been attributed to methine and/or methylene protons in branched and/or cyclized structures, while the latter peak has been attributed to methylene carbon atoms in the branched structure. Colorless polyacrylonitriles have been found to be predominantly heterotactic, while colored polyacrylonitriles have been found to have appreciable isotactic contribution.

Cyclic Peptide Disulfides - Solution And Solid-State Conformation Of Boc-Cys-Pro-Aib-Cys-S-S-Bridge-Nhme,A Disulfide-Bridged Peptide Helix

The solution and solid-state conformations of the peptide disulfide Boc-Cys-Pro-Aib-Cys-NHMe have been determined by NMR spectroscopy and X-ray diffraction. The Cys(4) and methylamide NH groups are solvent shielded in CDCI3 and (CD,),SO, suggesting their involvement in intramolecular hydrogen bonding. On the basis of known stereochemical preferences of Pro and Aib residues, a consecutive @-turn structure is favored in solution. X-ray diffraction analysis reveals a highly folded 310 helical conformation for the peptide, with the S-S bridge lying approximately parallel to the helix axis, linking residues 1 and 4. The backbone conformational angles are Cys(1) 4 = -121.1', $ = 65.6"; Pro(2) 4 = -58.9', 4 = -34.0'; Aib(3) 4 = -61.8', $ = -17.9'; Cys(4) 4 = -70.5', $ = -18.6'. Two intramolecular hydrogen bonds are observed between Cys(1) CO--HN Cys(4) and Pro(2) CO--HNMe. The disulfide bond has a right-handed chirality, with a dihedral angle (xss) of 82'.