No abstract

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°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.

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°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 γ+ and βt 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.

Proton NMR studies at 360 MHz are reported on the adenine dinucleoside monophosphates N6-dimethyladenyly(3'-5')-N6-dimethyladenosine (m(6)(2)Apm(6)(2)A), ApA, rApdA, dAprA and on the methyl phosphate esters of the monomers m(6)(2)Ap, pm(6)(2)A, Ap and pA. Complete 1H-NMR spectral assignments are given. The dimers were also investigated by means of circular dichroism to obtain accurate thermodynamic parameters of the stacking equilibrium. With the aid of the thermodynamic data NMR coupling constants are extrapolated to values appropriate to the stacked conformers. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the ribose and 2'-deoxyribose rings. It is shown that the unmethylated dimers can be arranged in two groups (dApdA/dAprA vs ApA/rApdA) according to their melting temperatures. ApA and the fully N6-methylated dimer m(6)(2)Apm(6)(2)A prefer to adopt the classical right-handed N-N stacked conformation. Both dimers with a 2'-deoxyribose ring at the 5'-OH end (dApdA and dAprA) behave similarly and occur in solution as a 75:25 mixture of S-S and S-N stacked states. The fully stacked hybrid dimer rApdA displays an unexpectedly large amount of S conformers (greater than 40%) in both sugar rings. This finding is rationalized by the postulation of a right-handed helical S-S stacked state on the basis of NMR and circular dichroic data.

A 500 MHz and 300 MHz NMR study of the trinucleoside diphosphate 3'd(A2'-5'A2'-5'A) is presented. In addition, circular dichroism is used to study base stacking in the title compound. The complete 1H-NMR spectral assignment of the sugar ring proton signals is given. Information about the sugar ring (N- or S-type conformation) and about the backbone geometry along C4'-C5' and C5'-O5' bonds is obtained from the NMR coupling constants. It is shown that the trimer mainly occurs in the N-N-N stacked state at low temperatures; the presence of a minor amount of N-N-S conformational sequence is indicated.