Ab-initio Quantum Mechanical Calculations of NMR Chemical Shifts in Nucleic Acid Constituents I The Watson-Crick Base Pairs

Abstract

The magnetic shielding constants of the different nuclei of the four nucleic acid bases adenine, uracile, guanine and cytosine are calculated by a non empirical method using a minimal basis set and compared to the available corresponding experimental data. The same calculations carried out for AU and GC pairs give not only the values of the chemical shift variations due to the formation of the pairs but also the relative importance of the three different contributions (geometric, polarization and charge transfer plus exchange) to the total value of Δδ Their analysis shows the importance of the polarization term. The magnitude of the charge transfer plus exchange term which is obtained for the nuclei belonging to the hydrogen bonding sites indicates that the hydrogen bond length is the major factor in the determination of the magnetic shielding constants of these atoms. On the other hand it appears that the pairing of the bases has a negligible effect on the “geometric” magnetic shielding due to the bases.     

13C NMR Chemical Shifts of the Triclinic and Monoclinic Crystal forms of Valinomycin

Two different crystalline polymorphs of valinomycin, the triclinic and monoclinic forms, have been studied by high resolution, solid state (13)C CP-MAS NMR spectroscopy. Although the two polymorphs of the crystal are remarkably similar, there are distinct differences in the isotropic chemical shifts between the two spectra. For the triclinic form, the carbon chemical shift tensor components for the alpha carbons adjacent to oxygen in the lactic acid and hydroxyisovaleric acid residues and the ester carbonyls of the valine residue were obtained using the FIREMAT experiment. From the measured components, it was found that the behavior of the isotropic chemical shift, delta(iso), for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, delta(22). Additionally it was found that the smallest shift component, delta(33), for the L -lactic acid ( L -Lac) and D -alpha-hydroxyisovaleric acid ( D -Hyi) C(alpha)-O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the delta(33) component that governs the behavior of delta(iso) in these alpha carbons.     

Ab-inito quantum mechanical calculations of NMR chemical shifts in nucleic acids constituents. II. Conformational dependence of the 1H and 13C chemical shifts in the ribose

The magnetic shielding constant of the different 13C and 1H nuclei of a deoxyribose are calculated for the C2' endo and C3' endo puckerings of the furanose ring as a function of the conformation about the C4'C5' bond. For the carbons the calculated variations are of several ppm, the C3' endo puckering corresponding in most cases to a larger shielding than the C2' endo one. For the protons the calculated variations of chemical shifts are all smaller than 1.3 ppm, that is of the order of magnitude of the variation of the geometrical shielding produced on these protons by the other units of a DNA double helix, with a change of the overall structure of the helix. The computations carried out on the deoxyribose-3' and 5' phosphates for several conformations of the phosphate group tend to show that the changes of conformation of the charged group of atoms produce chemical shift variations smaller than the two conformational parameters of the deoxyribose itself. The calculations carried out for a ribose do give the general features of the differences between the carbon and proton spectra of deoxynucleosides and nucleosides. The comparison of the measured and calculated phosphorylation shifts tend to show that the counterion contributes significantly, for some nuclei of the deoxyribose, to the shifts measured. The calculated magnitude of this polarization effect on carbon shifts suggests a tentative qualitative interpretation of carbon spectra of the ribose part of DNA double helices.     

Tautomerism,Protonation, and Ionization of Formycin in Aqueous Solution by the pH Dependence of 13C Chemical Shifts and 13C-1H Coupling Constants

Abstract

Analyses of the pH dependence of ¹³C chemical shifts and ¹³C-¹H coupling constants of formycin in aqueous soluion revealed two pKa′s, at 4.4 and 9.7, corresponding to a protonation at N₄ and an ionization at N₁. The N₄-protonation results in the transfer of a pyrazolo ring hydrogen from N₂ to N₂-At physiological pH, formycin was found to exist as a mixture of N₁H and N₂H tautomers, with the former being predominant (>94%).     

The Behaviour of Nucleic Acids and Other Constituents in Protomyces inundatus Dangeard

Estimations of contents per cell of DNA and RNA were made inProtomyces inundatus. There was twice as much DNA per cell incultures derived from fusion bodies and from mycelium in thehost (Apium nodiflorum) as in those derived from unfused endospores,indicating that the former two were diploid, the latter haploid.Dry weight/cell, volume/cell, insoluble nitrogen/cell, and metaphosphate/cell,like RNA/cell, had similar values for all three types of cultures.Giant cells resulting from camphor treatment not only had twiceas much DNA/cell as normal cultures derived from unfused endospores,but all the other characteristics studied had doubled as well.In any one culture the ratio of RNA to DNA remained constantthough the absolute values decreased as the cultures aged. TheRNA to DNA ratios in P. inundatus of haploid and diploid culturesare compared to those found in yeast and other organisms.     

Study of the Tautomerism by Experimentally and Theoretically Estimated 13C and 15N Chemical Shifts

2-Substituted 5-Me-7OH-1,2,4-Triazolo[1,5-a]pyrimidines can exist as different tautomeric forms. The tautomeric equilibrium of these compounds were determined by various NMR spectroscopic methods and quantum-chemical calculations. The tautomeric equilibria of 2-substituted 1,2,4-Triazolopyrimidines depend on the used solvent. In order to take solvent effects into account, ab initio calculations using the SCI-PCM method were carried out. The solvation energy depends on the polarity of the substituents in position 2. The comparison of chemical shifts determined by experimental methods and theoretical ab initio methods were used to definitely find out the the tautomeric equilibria of these compounds.     

Conformational Preferences of Modified Nucleic Acid Bases N6-Methyl-N6-(N-Threonylcarbonyl) Adenine and 2-Methylthio-N6-(N-Threonylcarbonyl) Adenine by the Quantum Chemical PCILO Calculations

Abstract

Conformational preferences of the hypermodified nucleic acid bases N⁶-methyl-N⁶-(N- threonylcarbonyl) Adenine, m⁶ tc⁶ Ade, and 2-methylthio-N⁶-(N-threonylcarbonyl) Adenine, mS² tc⁶ Ade, have been studied theoretically using the quantum chemical PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining the various torsion angles which take the favoured values obtained from energy variation with respect to each torsion angle individually. In m⁶ tc⁶ Ade and mS² tc⁶ Ade alike the threonylcar- bonyl substituent preferably orients away (distal) from the imidazole moiety of the adenine ring. And as in the simpler N⁶-(N-threonylcarbonyl) Adenine, tc⁶ Ade, the atoms in the ureido group as well as the amino acid carbon atoms C(12) and C(13) remain coplanar with the purine base. As in tc⁶ Ade, this conformation is stabilized by the intramolecular hydrogen bond between N(11)H of the amino acid and N(l) of the adenine base.

The N⁶-methyl protons, in m⁶ tc⁶ Ade, take trans-staggered orientation with respect to the C(6)-N(6) bond. The preferred orientation of the 2-methylthio group is cis to the C(2)-N(3) bond in mS² tc⁶ Ade. This is in marked contrast to the modified nucleic acid base 2-methylthio-N⁶-(Δ²-isopentenyl) Adenine, mS² i⁶ Ade, where the 2-methylthio group orients trans to the C(2)- N(3) bond, causing a change in the preferred orientation of the isopentenyl component on methylthiolation. The present results thus indicate that unlike in the isopentenyl adenine the role of further chemical substitutions in threonylcarbonyl adenine may be indirect and less pronounced.     

Carbon-13 NMR in Conformational Analysis of Nucleic Acid Fragments 2. A Reparametrization of the Karplus Equation for Vicinal NMR Coupling Constants in CCOP and HCOP Fragments

Abstract

¹³C-³¹P coupling constants of 10 oligoribonucleoside phosphates, measured at a number of temperatures, are presented. The combination of these data with ¹H-³¹ couplings of the same compounds leads to the derivation of two new and mutually consistent sets of Karplus parameters:

J(CCOP) = 6.9cos²φ - 3.4cosφ + 0.7

J(HCOP) = 15.3cos²φ - 6. 1cosφ + 1.6

At the same time new values for the base sequence dependent magnitude of the trans conformer of the backbone angle E ∈(C4′-C3′-03′-P) are calculated. The present results show that the magnitude of ∈(t) in right-handed ribo helices is confined to the range 214°-226° (average 219°), which is in much better agreement with single crystal X-ray studies (average 218°) than were previous deductions from NMR spectroscopic results (average 208°).     

Conformational transitions and fibrillation mechanism of human calcitonin as studied by high-resolution solid-state 13C NMR

Conformational transitions of human calcitonin (hCT) during fibril formation in the acidic and neutral conditions were investigated by high-resolution solid-state 13C NMR spectroscopy. In aqueous acetic acid solution (pH 3.3), a local alpha-helical form is present around Gly10 whereas a random coil form is dominant as viewed from Phe22, Ala26, and Ala31 in the monomer form on the basis of the 13C chemical shifts. On the other hand, a local beta-sheet form as viewed from Gly10 and Phe22, and both beta-sheet and random coil as viewed from Ala26 and Ala31 were detected in the fibril at pH 3.3. The results indicate that conformational transitions from alpha-helix to beta-sheet, and from random coil to beta-sheet forms occurred in the central and C-terminus regions, respectively, during the fibril formation. The increased 13C resonance intensities of fibrils after a certain delay time suggests that the fibrillation can be explained by a two-step reaction mechanism in which the first step is a homogeneous association to form a nucleus, and the second step is an autocatalytic heterogeneous fibrillation. In contrast to the fibril at pH 3.3, the fibril at pH 7.5 formed a local beta-sheet conformation at the central region and exhibited a random coil at the C-terminus region. Not only a hydrophobic interaction among the amphiphilic alpha-helices, but also an electrostatic interaction between charged side chains can play an important role for the fibril formation at pH 7.5 and 3.3 acting as electrostatically favorable and unfavorable interactions, respectively. These results suggest that hCT fibrils are formed by stacking antiparallel beta-sheets at pH 7.5 and a mixture of antiparallel and parallel beta-sheets at pH 3.3.     

Quantitative 13C NMR spectroscopy. Chemical structure of kraft and nitrosated lignins

Quantitative ¹³C NMR spectroscopy has been used to study the chemical structure of industrial kraft lignin, obtained from softwood pulping, and its nitrosated derivatives, which demonstrate high inhibition activity in the polymerization of unsaturated hydrocarbons.     

Reactions between Singlet Oxygen and the Constituents of Nucleic Acids: Importance of Reactions in Photodynamic Processes

Bases, nucleosides, nucleotides, and polynucleotides were exposed to chemically generated singlet oxygen to determine whether the species oxidized paralleled those oxidized in photodynamic reactions. In neutral or basic aqueous solution guanine, guanosine, deoxyguanosine, guanylic acid, deoxyguanylic acid, thymine, and uracil reacted with singlet oxygen. Since these compounds are oxidized in photodynamic processes, this study provides further evidence that singlet oxygen is the active intermediate in the photodynamic oxidation of nucleic acid constituents. Dienophilic attack by singlet oxygen is considered to be a plausible mechanism in these reactions.     

13 C NMR Chemical shifts and carbon-proton coupling constants of some furocoumarins and furochromones

The ¹³C NMR spectra of a variety of furocoumarins, dihydrofurocoumarins and furochromones are reported. The signals were assigned using carbon-proton coupling constants, ring annullation shifts, nuclear Overhauser effect considerations and shift effects caused by monothioester formation. Substituent effects on ¹³C chemical shifts and carbon-proton coupling constants are discussed. Methoxyl induced shifts of 5- and 8-substituted furocoumarins are additive, but their effects cannot be transferred to the furochromone system.     

Conformational exchange on the microsecond time scale in alpha-helix and beta-hairpin peptides measured by 13C NMR transverse relaxation

13C-NMR relaxation experiments (T(1), T(2), T(1)(rho), and NOE) were performed on selectively enriched residues in two peptides, one hydrophobic staple alpha-helix-forming peptide GFSKAELAKARAAKRGGY and one beta-hairpin-forming peptide RGITVNGKTYGR, in water and in water/trifluoroethanol (TFE). Exchange contributions, R(ex), to spin-spin relaxation rates for (13)C(alpha) and (13)C(beta) groups were derived and were ascribed to be mainly due to peptide folding-unfolding. To evaluate the exchange time, tau(ex), from R(ex), the chemical shift difference between folded and unfolded states, Deltadelta, and the populations of these states, p(i), were determined from the temperature dependence of (13)C chemical shifts. For both peptides, values for tau(ex) fell in the 1 micros to 10 micros range. Under conditions where the peptides are most folded (water/TFE, 5 degrees C), tau(ex) values for all residues in each respective peptide were essentially the same, supporting the presence of a global folding-unfolding exchange process. Rounded-up average tau(ex) values were 4 micros for the helix peptide and 9 micros for the hairpin peptide. This 2-3-fold difference in exchange times between helix and hairpin peptides is consistent with that observed for folding-unfolding of other small peptides.     

Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy

Group II chaperonin (CPN) cooperates with prefoldin (PFD), which forms a jellyfish-shaped heterohexameric complex with a molecular mass of 87 kDa. PFD captures an unfolded protein with the tentacles and transfers it to the cavity of CPN. Although X-ray crystal structures of CPN and PFD have been reported, no structural information has been so far available for the terminal regions of the PFD tentacles nor for the C-terminal segments of CPNs, which were regarded to be functionally significant in the previous studies. Here we report 13C NMR analyses on archaeal PFD, CPN, and their complex, focusing on those structurally uncharacterized regions. The PFD and CPN complexes selectively labeled with 13C at methionyl carbonyl carbons were separately and jointly subjected to NMR measurements. 13C NMR spectral data demonstrated that the N-terminal segment of the alpha and beta subunits of PFD as well as the C-terminal segments of the CPN hexadecamer retain significant degrees of freedom in internal motion even in the complex with a molecular mass of 1.1 MDa.     

Constituents of Papaver bracteatum: O-methyl-α-thebaol and 10-n-nonacosanol. Lanthanide-induced chemical shifts in 1H NMR and 13C NMR

Two non-alkaloidal constituents were identified in Papaver bracteatum: O-methyl-α-thebaol and 10-n-nonacosanol. O-Methyl-α-thebaol is a new natural compound. The presence of isothebaine is confirmed. Lanthanide-induced chemical shifts can be used for the assignments of the ₁₃C NMR chemical shifts of isothebaine and phenanthrenes. The use of lanthanide-induced chemical shifts in the identification of methoxyl resonances in ₁H NMR is discussed.     

Temperature Dependence of the Linkage of Quantum Yield of Photosystem II to CO2 Fixation in C4 and C3 Plants

The temperature dependence of quantum yields of electron transport from photosystem II (PSII) ([phi]II, determined from chlorophyll a fluorescence) and CO2 assimilation ([phi]CO2, apparent quantum yield for CO2 assimilation) were determined simultaneously in vivo. With C4 species representing NADP-malic enzyme, NAD-malic enzyme, and phosphoenolpyruvate carboxykinase subgroups, the ratio of [phi]II/[phi]CO2 was constant over the temperature range from 15 to 40[deg]C at high light intensity (1100 [mu]mol quanta m-2 s-1). A similar response was obtained at low light intensity (300 [mu]mol quanta m-2 s-1), except the ratio of [phi]II/[phi]CO2 increased at high temperature. When the true quantum yield for CO2 fixation ([phi]CO2*) was calculated by correcting for respiration in the light (estimated from temperature dependence of dark respiration), the ratio of [phi]II/[phi]C02* remained constant with varying temperature and under both light intensities in all C4 species examined. Because the [phi]II/[phi]CO2* ratio was the same in C4 monocots representing the three subgroups, the ratio was not affected by differences in the bio-chemical mechanism of concentrating CO2 in the bundle sheath cells. The results suggest that PSII activity is closely linked to the true rate of CO2 fixation in C4 plants. The close relationship between [phi]II and [phi]CO2* in C4 species under varying temperature and light intensity conditions is apparently due to a common low level of photorespiration and a primary requirement for reductive power in the C3 pathway. In contrast, in a C3 plant the [phi] II/[phi]CO2* ratio is higher under normal atmospheric conditions than under nonphotorespiratory conditions and it increases with rising temperature. This decrease in efficiency in utilizing energy derived from PSII for CO2 fixation is due to an increase in photorespiration. In both the C3 and C4 species, photochemistry is limited under low temperature, and thus excess energy must be dissipated by nonphotochemical means.     

Residue Specific Ribose and Nucleobase Dynamics of the cUUCGg RNA Tetraloop Motif by MNMR 13C Relaxation

The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with ¹³C and ¹⁵N were studied by ¹³C spin relaxation experiments. R₁, R_1ρ and the ¹³C-{¹H} steady-state NOE of C₆ and C_1′ in pyrimidine and C₈ and C_1′ in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational correlation time τ_c of 2.31±0.13 ns and an axial ratio of 1.35±0.02 were determined. Both findings are in agreement with hydrodynamic calculations. For the nucleobase carbons, the validity of different reported ¹³C chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539–10551; Fiala et al., 2000 J. Biomol. NMR 16, 291–302; Sitkoff, D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165–190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that all residues are mostly rigid (0.82 < S² < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution (S² = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from the analysis of ¹³C relaxation rates were found to be in agreement with ¹⁵N relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702–709). Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.