How S–C–N anomeric effects and energetic preference across [S–C–C–O] fragments steer conformational equilibria in 4′-thionucleosides. 1H NMR and ab initio MO study †

Abstract

Variable temperature-and pH-dependent 1 H NMR conformational analyses of 3 J HH coupling constants and NOE enhancements in the 4Ј-thionucleosides 1-10 in D 2 O, complemented by ab initio calculations, have given insight into the interplay of anomeric and other stereoelectronic effects that are modulated by the substitution of ring oxygen by sulfur in natural nucleosides. The N S pseudorotational equilibrium of the 2Ј-deoxy-4Ј-thionucleosides 1-4 is slightly shifted towards S-type conformers, while their ribo analogues 5-8 exhibit ca. 50 : 50 ratio at 278 K and neutral pH. α-4Ј-Thionucleosides 9 and 10 display a strong preference for N-type conformers. The S-C-N anomeric effect in 1-4 is stronger in purine than in pyrimidine 4Ј-thionucleosides, which is opposite to natural 4Ј-oxonucleosides, and increases in the following order: thymine < cytosine < guanine < adenine. The S-C-N anomeric effect in 1-4 is weaker than the O-C-N anomeric effect in their 4Ј-oxo counterparts. We have observed considerable population of up to 40% of γ Ϫ rotamers across the C4Ј-C5Ј bond, which has been attributed to the preference of the [S4Ј-C4Ј-C5Ј-O5Ј] fragments in 1-10 for trans over gauche conformation. Similarly, the 3Ј-OH group drives the N S equilibrium in 1-10 towards N where the [S4Ј-C4Ј-C3Ј-O3Ј] fragment adopts trans conformation. The 2Ј-OH group has been found to preferentially stabilise N-type sugar conformation in the 4Ј-thioribonucleosides 5-8 where it occupies a pseudoaxial orientation. The pK a values in 1-10 are almost identical to the pK a values of their natural counterparts, which shows that the acid-base character of the constituent heterocyclic moieties does not change upon substitution of oxygen with sulfur atom. The shift of the N S pseudorotational equilibrium in 1-8 towards N upon protonation and towards S upon deprotonation of the nucleobase is smaller by up to 10 percentage points in comparison to their 4Ј-oxo counterparts. This can be attributed to less efficient tuning of the S-C-N anomeric effect in 1-8 by protonation and deprotonation of the nucleobase. 1D difference NOE experiments indicated predominant anti orientation of the nucleobase in 2-10. Ab initio calculations at up to MP2/6-31G**//6-31G** level have shown two energy minima in the North and South regions of conformational space with the energy barriers between 17.5 and 28.5 kJ mol Ϫ1 in the East region. Interestingly, the energy barrier in the West region is comparable or even lower than the barrier in the East region of conformational space in 1-10, which is in contrast to natural nucleosides.

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

“…According to ab initio calculations for 1-methoxy-2-(methylsulfanyl)ethane, the antiperiplanar conformation of the SÀCÀCÀO fragment is favoured over a synclinal conformation by 0.13 kcal/mol, close to the experimental value of 0.17 kcal/mol [19]. We used the average value of 0.15 kcal/mol.…”

Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine

“…The presence of sulfur at the 4′-position can be expected to change the pseudorotational equilibrium in the ribose moiety. For example, the gauche effect for [S-C-C-O] fragments is most probably weaker compared with the 4′-oxo counterparts because sulfur is less electronegative than oxygen (23). The S4′-C1′-N9/1 anomeric effect is weaker in pyrimidines than in purines (23), whereas the situation is reversed in the case of 4′-oxonucleosides (24).…”

“…For example, the gauche effect for [S-C-C-O] fragments is most probably weaker compared with the 4′-oxo counterparts because sulfur is less electronegative than oxygen (23). The S4′-C1′-N9/1 anomeric effect is weaker in pyrimidines than in purines (23), whereas the situation is reversed in the case of 4′-oxonucleosides (24). Overall, the S4′-C1′-N9/1 anomeric effect is weaker than the O4′-C1′-N9/N1 one.…”

“…Similar to the effect of the 2′-hydroxyl group on the sugar conformation in 4′-oxonucleosides, where an electronegative 2′-substituent stabilizes a C3′- endo (N) type pucker, the N-type rotamer is preferred by 4′-thioribonucleosides compared with 4′-thio-2′-deoxyribonucleosides. For example, solution NMR experiments revealed a ΔΔ H ° of 3.8 kJ mol −1 between 4′-thio-C and 4′-thio-2′-deoxyribo-C in favor of the modified ribonucleoside (23). More recently, the relative overall order of thermal stabilities of duplexes was reported to be 4′-thio-RNA:4′-thio-RNA ≫ 4′-thio-RNA:RNA > RNA:RNA > RNA:DNA > 4′-thio-RNA:DNA (25).…”

Unexpected A-form formation of 4′-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance

“…Some work in this respect has been done on nucleosides (35,36). The changes of these effects may also contribute to the formation of the A-form for fully modified 4′-thioDNA, although the rational interpretation is not available at this moment.…”