13C−1H and 13C−13C Spin Couplings in [2‘-13C]2‘-Deoxyribonucleosides: Correlations with Molecular Structure

Enzymatic synthesis of ribo- and 2'-deoxyribonucleosides from glycofuranosyl phosphates: An approach to facilitate isotopic labeling

Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by ¹H and ¹³C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 °C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate. This methodology is attractive for the preparation of stable isotopically labeled ribo- and 2'-deoxyribonucleosides because of the ease of product purification and convenient use and recycling of nitrogen bases. The approach eliminates the need for separate reactions to prepare individual furanose-labeled ribonucleosides, since only one ribonucleoside (inosine) needs to be labeled, if desired, in the furanose ring, the latter achieved by a high-yield chemical N-glycosylation. 2'-Deoxyribonucleosides were prepared from 2'-deoxyinosine using the same methodology with minor modifications.

Comparison between DFT- and NMR-based conformational analysis of methyl galactofuranosides

Galactofuranose (Galf) residues are found in a number of microbial polysaccharides, and knowledge of their conformation is key for developing a molecular-level understanding of their biological roles. To this end, we studied 180 conformations of methyl α- and β-Galf in aqueous solution (COSMO solvation model) using density functional theory (DFT). We compare the calculated low energy conformations to those determined from the program PSEUROT using (1)H NMR data. The lowest energy ring conformation for methyl α-Galf is (2)E, and this conformer is also the major solution conformation obtained by NMR spectroscopy. For methyl β-Galf, (4)E is the lowest energy ring conformation; however, DFT results do not agree with the solution NMR spectroscopic results. Additionally, we developed Galf-specific Karplus-like equations from these conformations.

Correlation of (2)J couplings with protein secondary structure

Geminal two-bond couplings ((2)J) in proteins were analyzed in terms of correlation with protein secondary structure. NMR coupling constants measured and evaluated for a total six proteins comprise 3999 values of (2)J(CalphaN'), (2)J(C'HN), (2)J(HNCalpha), (2)J(C'Calpha), (2)J(HalphaC'), (2)J(HalphaCalpha), (2)J(CbetaC'), (2)J(N'Halpha), (2)J(N'Cbeta), and (2)J(N'C'), encompassing an aggregate 969 amino-acid residues. A seamless chain of pattern comparisons across the spectrum datasets recorded allowed the absolute signs of all (2)J coupling constants studied to be retrieved. Grouped by their mediating nucleus, C', N' or C(alpha), (2)J couplings related to C' and N' depend significantly on phi,psi torsion-angle combinations. beta turn types I, I', II and II', especially, can be distinguished on the basis of relative-value patterns of (2)J(CalphaN'), (2)J(HNCalpha), (2)J(C'HN), and (2)J(HalphaC'). These coupling types also depend on planar or tetrahedral bond angles, whereas such dependences seem insignificant for other types. (2)J(HalphaCbeta) appears to depend on amino-acid type only, showing negligible correlation with torsion-angle geometry. Owing to its unusual properties, (2)J(CalphaN') can be considered a "one-bond" rather than two-bond interaction, the allylic analog of (1)J(N'Calpha), as it were. Of all protein J coupling types, (2)J(CalphaN') exhibits the strongest dependence on molecular conformation, and among the (2)J types, (2)J(HNCalpha) comes second in terms of significance, yet was hitherto barely attended to in protein structure work.

Collective headgroup conformational transition in twisted micellar superstructures

Predictions on amphiphilic self-assemblies traditionally rely on considerations on molecular shape and charge of the surfactant. In the case of functional surfactants a more sophisticated toolbox becomes necessary to design amphiphiles encoding chemical functionalities that provide additional responsive properties to their self-assemblies. Here we report on a comprehensive and combined structural-spectroscopic characterization of 1,2-dilauroyl-phosphatidyl-adenosine (DLPA) micelles in phosphate buffer. The temperature dependence, more precisely the thermal history of the sample, is explicitly taken into account. The experimental data, supplemented with MD simulations, indicate the presence of two possible states at room temperature, characterized by distinctly different structural properties that depend on the thermal history of the sample. The twisted superstructures, produced by aging DLPA micelles through intermicellar assembly of locally cylindrical aggregates at room temperature, collapse upon warming at 35 °C, yielding aligned filaments and/or wormlike structures. The initial superstructures cannot be recovered by thermal inversion. The reason for this behaviour is that the thermal activation causes a redistribution of syn-anti conformations of adenosine headgroups, as indicated by spectroscopic results (NMR, CD, FTIR), which is then collectively frozen thanks to molecular constraints present in the aggregate.

Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides

The eight nucleoside constituents of nucleic acids were simulated for 50 ns in explicit water with molecular dynamics. This provides equilibrium populations of the torsional degrees of freedom, their kinetics of interconversion, their couplings, and how they are influenced by water. This is important, given that a full and quantitative characterization of the nucleosides in aqueous solution by experimental means has been elusive, despite immense efforts in that direction. It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. The glycosidic torsion distributions in the anti conformation are strongly affected by water and depart from the corresponding X-ray modal values and the associated energy minima in vacuo. Water also preferentially stabilizes some sugar conformations, showing that potential energies in vacuo are not sufficient to understand the nucleosides. Deoxythymidine (but not other pyrimidines) significantly populates the syn orientation. Guanine favors the syn orientation more than adenine. The ribose favors the syn orientation significantly more than the deoxyribose. The NORTH pucker coexists with the syn conformers. A hydrogen bond is frequently formed between the 5'-OH group and the syn bases, despite competition by water. The rate of the anti/syn transitions with purines is on the nanosecond time scale, confirming a long held assumption underpinning the interpretation of ultrasonic relaxation studies. Therefore, our knowledge of the structure and dynamics of nucleosides in solvent is only limited by the accuracy of the potential used to simulate them, and it is shown that such simulations provide a distinct and unique test of nucleic acid force fields. This confirmed that the widely distributed CHARMM27 force field is, overall, well-balanced with a particularly good representation of the ribose. Specific improvements, however, are suggested for the deoxyribose and torsion gamma.

[13C,15N]2-Acetamido-2-deoxy-d-aldohexoses and Their Methyl Glycosides: Synthesis and NMR Investigations of J-Couplings Involving 1H, 13C, and 15N

[reaction: see text] A series of 2-amino-2-deoxy-D-[1-13C]aldohexoses and their methyl glycosides was prepared with use of a simplified cyanohydrin reduction route. Four d-aldopentosylamines (arabino, lyxo, ribo, xylo) were prepared from the corresponding D-aldopentoses by reaction with NH3(g) in MeOH solvent, isolated in solid form, and characterized by 13C and 1H NMR. Hydrolysis of beta-D-xylopyranosylamine was studied using 13C-labeled substrates to establish optimal solution conditions for cyanohydrin formation. Major hydrolytic intermediates were observed and identified by time-lapse 1D and 2D NMR analyses of reaction mixtures. The aldopentosylamines were subsequently employed in cyanohydrin reduction reactions with K13CN to yield C2-epimeric [1-13C]2-aminosugars, which were separated by chromatography on ion-exchange columns. N-Acetylation and methyl glycosidation followed by chromatography gave pure 2-acetamido-2-deoxy-D-[1-13C]aldohexopyranosides. J(CH) and J(CC) spin-spin coupling constants involving the labeled anomeric carbon were measured and compared to those observed previously in methyl D-[1-13C]aldohexopyranosides. In parallel studies, theoretical J-couplings were calculated in model N-acetylated aldopyranosides using density functional theory (DFT) to predict the effect of OH vs NHCOCH(3) substitution at C2 on J(CH) and J(CC) values in aldopyranosyl rings. The synthetic method was also modified to accommodate (15)N- and (13)C-labeling within the N-acetyl side-chain, and some J-couplings involving 1H, 13C, and 15N atoms in 2-[1,2-13C2;15N]acetamido-2-deoxy-D-[1-13C]glucose were measured and interpreted.

Correlated C-C and C-O bond conformations in saccharide hydroxymethyl groups: parametrization and application of redundant 1H-1H, 13C-1H, and 13C-13C NMR J-couplings

Methyl alpha- and beta-pyranosides of d-glucose and d-galactose 1-4 were prepared containing single sites of (13)C-enrichment at C4, C5, and C6 (12 compounds), and (1)H and (13)C[(1)H] NMR spectra were obtained to determine a complete set of J-couplings ((1)J, (2)J, and (3)J) involving the labeled carbon and nearby protons and carbons within the exocyclic hydroxymethyl group (CH(2)OH) of each compound. In parallel theoretical studies, the dependencies of (1)J, (2)J, and (3)J involving (1)H and (13)C on the C5-C6 (omega) and C6-O6 (theta;) torsion angles in aldohexopyranoside model compounds were computed using density functional theory (DFT) and a special basis set designed to reliably recover the Fermi contact contribution to the coupling. Complete hypersurfaces for (1)J(C5,C6), (2)J(C5,H6)(R), (2)J(C5,H6)(S), (2)J(C6,H5), (2)J(C4,C6), (3)J(C4,H6)(R), (3)J(C4,H6)(S), and (3)J(C6,H4), as well as (2)J(H6)(R)(,H6)(S), (3)J(H5,H6)(R), and (3)J(H5,H6)(S), were obtained and used to parametrize new equations correlating these couplings to omega and/or theta;. DFT-computed couplings were also tested for accuracy by measuring J-couplings in (13)C-labeled 4,6-O-ethylidene derivatives of d-glucose and d-galactose in which values of omega and theta; were constrained. Using a new computer program, Chymesa, designed to utilize multiple J-couplings sensitive to exocyclic CH(2)OH conformation, the ensemble of experimental couplings observed in 1-4 were analyzed to yield preferred rotamer populations about omega and theta;. Importantly, due to the sensitivity of some couplings, most notably (2)J(H6)(R)(,H6)(S), (2)J(C5,H6)(R), and (2)J(C5,H6)(S), to both omega and theta;, unique information on correlated conformation about both torsion angles was obtained. The latter treatment represents a means of evaluating correlated conformation in 1,6-linked oligosaccharides, since psi and theta; are redundant in these linkages. In the latter regard, multiple, redundant scalar couplings originating from both sides of the glycosidic linkage can be used collectively to evaluate conformational correlations between psi/theta; and C5-C6 bond rotamers.

J-modulated ADEQUATE (JM-ADEQUATE) experiment for accurate measurement of carbon-carbon coupling constants

A new method for the accurate determination of carbon-carbon coupling constants is described. The method is based on a modified ADEQUATE experiment, where a J-modulated spin-echo sequence precedes the ADEQUATE pulse scheme. The J-modulation and scaling of carbon-carbon couplings is based on simultaneous incrementation of 13C chemical shift and coupling evolution periods. The time increment for the homonuclear carbon-carbon coupling evolution can be suitably scaled with respect to the corresponding increment for the chemical shift evolution. Typically a scaling factor of 2 to 3 is employed for the measurement of one-bond coupling constants, while multiplication by a factor of 10 to 15 is applied when small long-range couplings are determined. The same pulse scheme with coupling evolution period optimized for one-bond or long-range couplings allows the determination of the corresponding carbon-carbon coupling constants. The splittings of the ADEQUATE crosspeaks in the F1 dimension yield the appropriately multiplied coupling constants.

DFT analysis of NMR scalar interactions across the glycosidic bond in DNA

The relationship between the glycosidic torsion angle chi, the three-bond couplings (3)J(C2/4-H1') and (3)J(C6/8-H1'), and the one-bond coupling (1)J(C1'-H1') in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and chi depend strongly on the aromatic base. (3)J(C2/4-H1') reveals different behavior for deoxyadenosine, deoxyguanosine, and deoxycytidine as compared to deoxythymidine and deoxyuridine. In the case of (3)J(C6/8-H1'), an opposite trans to cis ratio of couplings is obtained for pyrimidine nucleosides in contrast to purine nucleosides. The extremes of the Karplus curves are shifted by ca. 10 degrees with respect to syn and anti-periplanar orientations of the coupled nuclei. The change in the sugar pucker from S to N decreases (3)J(C2/4-H1') and (3)J(C6/8-H1'), while increasing (1)J(C1'-H1') for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. The influence of the sugar pucker on (1)J(C1'-H1') is interpreted in terms of interactions between the n(O4'), sigma*(C1'-H1') orbitals. The (1)J(C1'-H1') are related to chi through a generalized Karplus relationship, which combines cos(chi) and cos(2)(chi) functions with mutually different phase shifts that implicitly accounts for a significant portion of the related sugar pucker effects. Most of theoretical (3)J(C2/4-H1') and (3)J(C6/8-H1') for uracil cyclo-nucleosides compare well with available experimental data. (3)J(C6/8-H1') couplings for all C2-bridged nucleosides are up to 3 Hz smaller than in the genuine nucleosides with the corresponding chi, revealing a nonlocal aspect of the spin-spin interactions across the glycosidic bond. Theoretical (1)J(C1'-H1') are underestimated with respect to the experiment by ca. 10% but reproduce the trends in (1)J(C1'-H1') vs chi.

Conformational studies of methyl 3-O-methyl-alpha-D-arabinofuranoside: an approach for studying the conformation of furanose rings

A computational method for probing furanose conformation has been developed using a methylated monosaccharide derivative 1. First, a large library of conformers was generated by a systematic pseudo Monte Carlo search followed by optimization with the AMBER molecular mechanics force field. A subset of these conformers was then subjected to ab initio and density functional theory calculations in both the gas and aqueous phases. These calculations indicate that entropic contributions to the Gibbs free energy are important determinants of the Boltzmann distribution for the conformational preferences of 1 in the gas phase. The results obtained at each level of theory are discussed and compared with the experimentally determined conformer distribution from NMR studies in aqueous solution. In addition, the ability of each level of theory to reproduce the experimentally measured 1H-1H coupling constants in 1 is discussed. Empirical Karplus equations and density functional theory methods were used to determine average 3J(H1,H2), 3J(H2,H3), and 3J(H3,H4) for each level of theory. On the basis of this comparison, consideration of solvation with the MN-GSM model provided good agreement with the experimental data.

Effect of substitution pattern on 1H, 13C NMR chemical shifts and 1J(CH) coupling constants in heparin derivatives

1H, 13C NMR chemical shifts and 1J(CH) coupling constants were measured for derivatives of heparin containing various sulfation patterns. 1H and 13C chemical shifts varied considerably after introducing electronegative sulfate groups. Chemical shifts of protons linked to carbons changed by up to 1 ppm on substitution with O- and N-sulfate or acetyl groups. Differences up to 10 ppm were detected for 13C chemical shifts in substituted glucosamine, but a less clear dependence was found in iduronate. 1J(CH) values formed two groups, corresponding to either sulfation or non-sulfation at positions 2 and 3 of glucosamine. O-sulfation caused increases up to 6 Hz in 1J(CH) and N-sulfation decreases up to 4 Hz. N-acetylation gave similar 1J(CH) values to N-sulfation. At positions 2 and 3 of iduronate the trend was less marked; 1J(CH) for O-sulfated positions usually increasing. Introduction of sulfate groups influences chemical shift and 1J(CH) values at the position of substitution, but also at more remote positions. 1J(CH) at the glycosidic linkage positions varied between free-amino and N-sulfated compounds, by up to 9 Hz. These results and changes in chemical shift values suggest that iduronate residues and the glycosidic linkages are affected, indicating overall conformational change. This may have important implications for biological activities.

Probing furanose ring conformation by gas-phase computational methods: energy profile and structural parameters in methyl beta-D-arabinofuranoside as a function of ring conformation

The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.

13C-labeled platinum(IV)-carbohydrate complexes: structure determination based on (1)H-(1)H, (13)C-(1)H, and (13)C-(13)C spin-spin coupling constants

The reaction of D-mannose and D-allose with [PtMe(3)(Me(2)CO)(3)]BF(4) 1 in acetone affords complexes [PtMe(3)L]BF(4) 5 and 6 (5, L = alpha-D-mannofuranose; 6, L = beta-D-allofuranose). The coordination mode and conformation of the carbohydrate ligands in 5 and 6 in acetone-d(6) have been determined from an analysis of J(HH), J(CH), and J(CC) in complexes formed using site-specific (13)C-labeled D-mannose and D-allose. These coupling data are compared to those measured in (13)C-labeled complex [PtMe(3)L]BF(4) 2 (L = 1, 2-O-isopropylidene-alpha-D-glucofuranose) and 1, 2-O-isopropylidene-alpha-D-glucofuranose 3, whose solid-state structures are known, and in (13)C-labeled 1,2;5, 6-di-O-isopropylidene-alpha-D-glucofuranose 4. The preferred furanose ring conformations in 2 and 5 are very similar ((3)E/E(4) and E(4)/(o)E/E(1), respectively; eastern hemisphere of the pseudorotational itinerary), with platinum coordination involving O3, O5, and O6 of the saccharide. In contrast, the furanose ring of 6 prefers an (4)E/E(o)/(1)E geometry (western hemisphere of the pseudorotational itinerary) resulting from altered complexation involving O1, O5, and O6. Couplings within the exocyclic fragments of 2, 5, and 6 also support the existence of two different platinum coordination modes. In addition to establishing the structures and conformations of 2, 5, and 6 in solution, one-, two-, and three-bond J(CH) and J(CC) observed in these complexes provide new insights into the effect of structure and conformation on the magnitudes of these couplings in saccharides. Weak platinum(IV) complexation with the carbohydrate conformationally restricts the furanose and exocyclic fragment without introducing undesirable structural strain, thereby allowing more reliable correlations between structure and coupling magnitude.

Configurative correlation and conformational analysis of strictosidine and vincoside derivatives

On the basis of the configuration of C-15 of the secologanin unit, using detailed NMR analysis, the configuration of C-3, the solution conformation around C-14, and the glucosidic bridge, as well as those of the dihydropyran and tetrahydropyridine rings, were determined in the vincosamide and strictosamide derivatives 4b and 5b. The stereochemical analysis was extended by chemical correlation to the 4-benzylated strictosidine and vincoside derivatives 3c and 3d. Experimental proof was presented for the interpretation of the "anomalous" chemical shift of acetylated strictosamide derivatives.

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

Structural properties of biomolecules are dictated by their intrinsic conformational energetics in combination with environmental contributions. Calculations using high-level ab initio methods on the deoxyribonucleosides have been performed to investigate the influence of base on the intrinsic conformational energetics of nucleosides. Energy minima in the north and south ranges of the deoxyribose pseudorotation surfaces have been located, allowing characterization of the influence of base on the structures and energy differences between those minima. With all bases, chi values associated with the south energy minimum are lower than in canonical B-DNA, while chi values associated with the north energy minimum are close to those in canonical A-DNA. In deoxycytidine, chi adopts an A-DNA conformation in both the north and south energy minima. Energy differences between the A and B conformations of the nucleosides are <0.5 kcal/mol in the present calculations, except with deoxycytidine, where the A form is favored by 2.3 kcal/mol, leading the intrinsic conformational energetics of GC basepairs to favor the A form of DNA by 1.5 kcal/mol as compared with AT pairs. This indicates that the intrinsic conformational properties of cytosine at the nucleoside level contribute to the A form of DNA containing predominately GC-rich sequences. In the context of a B versus Z DNA equilibrium, deoxycytidine favors the Z form over the B form by 1.6 kcal/mol as compared with deoxythymidine, suggesting that the intrinsic conformational properties of cytosine also contribute to GC-rich sequences occurring in Z DNA with a higher frequency than AT-rich sequences. Results show that the east pseudorotation energy barrier involves a decrease in the furanose amplitude and is systematically lower than the inversion barrier, with the energy differences influenced by the base. Energy barriers going from the south (B form) sugar pucker to the east pseudorotation barrier are lower in pyrimidines as compared with purines, indicating that the intrinsic conformational properties associated with base may also influence the sugar pseudorotational population distribution seen in DNA crystal structures and the kinetics of B to A transitions. The present work provides evidence that base composition, in addition to base sequence, can influence DNA conformation.