The interaction of the 2′-OH group with the vicinal phosphate in ribonucleoside 3′-ethylphosphate drives the sugar-phosphate backbone into unique (S,ω −) conformational state

Abstract

The analysis of temperature-dependent vicinal proton-proton coupling constants has shown that the North (N)South (S) pseudorotational equilibria of ribonucleoside 3′-ethylphosphates [ApEt ( 21), GpEt ( 22), CpEt( 23), rTpEt ( 24) and UpEt ( 25)], modelling simple diribonucleoside(3′ → 5′)monophosphate without any intramolecular base-base stacking, are driven more towards the South-type sugar (S) by ΔΔ11° = −2.5 kJ mol −1 in the case of purine and by ≈ −3.8 kJ mol −1 in the case of pyrimidine nucleotides compared to the corresponding parent ribonucleosides 1 - 5. In contrast, the S-type sugar conformation in 2′-deoxyribonucleoside 3′-ethylphosphates (ref. 3d) is stabilized by ΔΔH ° ≈ −1.9 kJ mol −1 in both purine and pyrimidine nucleotides compared to the parent 2′-deoxyribonucleosides. The total energetic effect of 2′-OH group due to its interaction with the vicinal phosphate in ribonucleotides in contrast with the corresponding 2′ -deoxynucleotide counterparts can be assessed by subtracting the free-energies of NS pseudorotational equilibria in the ribonucteotide analogs 21 – 25 from the corresponding 2′-deoxynucleotide counterparts 16 – 20: ΔΔG 298 ≈ +0.3 kJ mol −1 in ApEt ( 21), +0.6 kJ mol −1 in GpEt ( 22), +2.1 kJ mol −1 CpEt ( 23), +1.1 kJ mol −1 in rTpEt (24) and +1.3 kJ mol −1 in UpEt (25). The additional stabilization of the S-type pseudorotamers in ribonucleoside 3′-ethylphosphates 21 – 25 compared to ribonucleoside 3′-monophosphates 11–15 by ΔΔH ° ≈ -2.0 kJ mol −1 is attributed to the influence of the 2′-OH group in the former. The population of ω 1 rotamers increases by 7–13% from 278 to 358K, which corresponds also with an equal increase of the population of N-type pseudorotamers, suggesting a unique cooperativity in the two-state (N,ω 1)(S,ω −) conformational equilibria in 21 – 25. These cooperative conformational transitions of (N,ω 1)(S,ω −) equilibrium in 21 – 25 have been found to be orchestrated by the interaction of 2′-hydroxyl group with the vicinal phosphate as evident by the non-equivalent methylene protons of the 3′-ethylester function uplo 348K in 21 – 25 compared to the 2′-deoxynucleotide counterparts 16 – 20 (ref. 3d). The intramolecular interaction of the 2′-OH function with the vicinal phosphodiester stabilizes the S and ω − conformers (“On” switch), whereas 2′-OH in a non-interacting stale stabilizes the N and ω 1 conformers (“Off switch) in 21 – 25. The strengths of this “On-Off” molecular switch for the preference of (S,ω −) conformational slate over (N,ω 1) slate in 21 – 25 are as follows: ΔG 298 ≈ −2.8 kJ mol −1 for adenosine 3′-ethylphosphate ( 21), −2.1 kl mol −1 for guanosine 3′-ethylphosphate (22), ≈ 0.1 kJ mol −1 for cytidine 3′-ethylphosphate ( 23), −0.9 kJ mol −1 for ribothymidine 3′-ethylphosphate ( 24) and −0.7 kJ mol −1 for uridine 3′-ethylphosphaie ( 25).