Adenylyl-uridine. Assignment and analysis of the 270 Mhz fast Fourier transform proton magnetic resonance spectrum

Conformational analysis of the single-stranded ribonucleic acid A-A-C-C. A one-dimensional and two-dimensional proton NMR study at 500 MHz

Proton NMR studies at 300 MHz and 500 MHz are reported on the ribotetranucleotide A-A-C-C. The complete 1H-NMR spectral assignment at 20 degrees C is given. Two-dimensional NMR was used to elucidate spin multiplets in 'crowded' regions. Nuclear Overhauser enhancement (NOE) experiments made an unambiguous spectral assignment possible and yielded information on interproton distances. The N/S equilibrium of the riboses and the rotamer populations around some backbone torsion angles are presented. A large preference for N-type ribose and gamma+ and beta t backbone torsions is observed, in particular in the central A-C unit of A-A-C-C. Information on distances between protons of different nucleotide units, obtained from NOE experiments, constitutes a probe of base-base stacking. It is concluded that A-A-C-C offers a good model for RNA single-strand conformation.

Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method

Chemical shifts of base and sugar protons of the modified ribodinucleoside monophosphate N6-dimethyladenylyl(3'-5')uridine (m2(6)A-U) were measured at 100, 360 and 400 MHz in aqueous solution. Seven different samples were used with concentrations ranging from 0.28 mM to 32.7 mM. The temperature was varied from -5 degrees C to 105 degrees C. An internal temperature calibration was used. The effects of intermolecular self-association and of intramolecular stacking on the chemical shifts were quantitatively separated by means of a new approach: differential concentration/temperature profiles (DCTP). Several computational models were tested and the analysis allowed deeper insight into the behaviour of m2(6)A-U at the molecular level. The simple two-state approach for both self-association and stacking already afforded a significant improvement over models in which the association is entirely neglected. A computer least-squares analysis of the chemical shift behaviour of each individual proton yielded thermodynamic parameters for self-association and stacking. However, the two-state model did not suffice to reproduce accurately all of the observations. A satisfactory fit required two additional assumptions: (a) the aromatic protons experience different association shifts in stacked and in unstacked molecules: (b) a temperature-dependent conformational equilibrium exists between sets of unstacked microstates. The stacked state is taken to represent a single conformational species. The implementation of this extended model in the least-squares optimization allowed the reproduction of over one thousand chemical shift observations within experimental error. Thermodynamic equilibrium parameters deduced for intramolecular stacking are: delta H degrees x = -28.8 kJ mol-1, delta S degrees x = -93 J mol-1 K-1. These numbers agree well with those obtained earlier by us from circular dichroism spectra. The equilibrium enthalpy and entropy values deduced for the association process are: delta H degrees A = -35 kJ mol-1 and delta S degrees A = -95 J mol-1 K-1.

Conformational analysis of the nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from nuclear magnetic resonance and circular dichroism studies

In recent publications A2'-5'A2'-5'A was found to be an inhibitor of protein synthesis. In this research conformational analysis of the 2'-5'-linked nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U is reported. The complete 1H-NMR assignment of the three compounds is given. The degree and mode of base-base stacking is extracted from coupling constant data and circular dichroic (CD) spectra at various temperatures. The 2'-5' nucleotides surprisingly show a much stronger tendency to stack than the 3'-5' compounds. At 85 degrees C A2'-5'A occurs for about 50% in stacked states. The mode of stacking is different from 3'-5'ribonucleotides where the sugar rings predominantly adopt an N conformation. A2'-5'U displays an A(S)2'-5'U(N) stacked state. In A2'-5'A 'mixed' modes of stacking, i.e. NN, NS, SN and SS, are proposed to account for the CD and NMR observations.

Circular dichroism studies of 6-N-methylated adenylyladenosine and adenylyluridine and their parent compounds. Thermodynamics of stacking

The temperature dependence of the circular dichroism spectra of two adenylyladenosine and three adenylyluridine dinucleotides in aqueous solution have been studied. The effect of methylation of the N-6 position of the adenylyl moieties on the thermodynamic parameters of the stacking equilibrium was investigated applying a two-state model for the thermodynamic analysis of the experimental data. It is shown that the methylated compounds allow a more accurate analysis of the data and that methylation stabilizes the stacking interaction by a relative decrease of the entropy of unstacking.

Oligonucleotide conformations. (5) NMR and relaxation studies on GpU and UpG at neutral pH

The average conformation of GpU and UpG in neutral aqueous solutions has been investigated by proton chemical shifts and coupling measurements as well as T1 relaxation time experiments. The proportion of the N and S pseudorotational conformers of the ribose ring has been derived from the vicinal coupling constants. The relaxation data provide information about the syn--anti equilibrium of the orientation of the base about the glycosidic bond. This orientation is predominantly syn for the Guo base in both dinucleoside phosphates, that of Urd is anti in the case of GpU and shows an almost equivalent syn and anti character for UpG.

Conformational analysis of a DNA triplet in aqueous solution. Thymidylyl-(3'-5')-thymidylyl-(3'-5')-2'-deoxyadenosine, d(T-T-A), studied by 1H nuclear magnetic resonance at 360 MHz

The proton signals of a 50 mM solution of thymidylyl-(3'-5')-thymidylyl-(3'-5')-2'-deoxyadenosine, d(T-T-A), in 2H2O at 65 degrees C and p2H=7.4, were detected by nuclear magnetic resonance at 360 MHz. Complete assignment of the 21 ribose proton signals was achieved by extensive decoupling experiments and computer simulations. The coupling constant data show that the ribose rings prefer to adopt the S (2'-endo) conformation. The presence of a substantial amount of a right handed helical structure of the d(-T-A) fragment is indicated from chemical shift considerations. The molecule displays a high degree of conformational purity along the sugar-phosphate backbone.