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The hydrogen bonding and hydration of 2′-OH in adenosine and adenosine 3′-ethyl phosphate

The hydrogen bonding and hydration of 2′-OH in adenosine and adenosine 3′-ethyl phosphate

Acharya, Parag ORCID: 0000-0003-2521-9968 and Chattopadhyaya, Jyoti B (2002) The hydrogen bonding and hydration of 2′-OH in adenosine and adenosine 3′-ethyl phosphate. Journal of Organic Chemistry, 67 (6). pp. 1852-1865. ISSN 0022-3263 (Print), 1520-6904 (Online) (doi:

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The 2‘-OH group has major structural implications in the recognition, processing, and catalytic properties of RNA. We report here intra- and intermolecular H-bonding of 2‘-OH in adenosine 3‘-ethyl phosphate (1), 3‘-deoxyadenosine (2), and adenosine (3) by both temperature- and concentration-dependent NMR studies, as well as by detailed endo (3JH,H) and exocyclic (3JH,OH) coupling constant analyses. We have also examined the nature of hydration and exchange processes of 2‘-OH with water by a combination of NOESY and ROESY experiments in DMSO-d6 containing 2 mol % HOD. The NMR-constrained molecular modeling (by molecular mechanics as well as by ab initio methods both in the gas and solution phase) has been used to characterize the energy minima among the four alternative dihedrals possible from the solution of the Karplus equation for 3JH2‘,OH and 3JH3‘,OH to delineate the preferred orientation of 2‘-O-H proton in 1 and 2 as well as for 2‘/3‘-O-H protons in 3. The NMR line shape analysis of 2‘-OH gave the Δ of 7.5 kJ mol-1 for 1 and 8.4 kJ mol-1 for 3; similar analyses of the methylene protons of 3‘-ethyl phosphate moiety in 1 also gave comparable Δ of 7.3 kJ mol-1. The donor nature of the 2‘-OH in the intramolecular H-bonding in 3 is evident from its relatively reduced flexibility [−TΔS⧧]2‘-OH = −17.9(±0.5) kJ mol-1] because of the loss of conformational freedom owing to the intramolecular 2‘O-H···O3‘ H-bonding, compared to the acceptor 3‘-OH in 3 [−TΔS⧧]3‘-OH = −19.8 (± 0.6) kJ mol-1] at 298 K. The presence of intramolecular 2‘-OH···O3‘ H-bonding in 3 is also corroborated by the existence of weak long-range 4JH2‘,OH3‘ in 3 (i.e., W conformation of H2‘−C2‘−C3‘−O3‘−H) as well as by 3JH,OH dependent orientation of the 2‘- and 3‘-OH groups. The ROESY spectra for 1 and 3 at 308 K, in DMSO-d6, show a clear positive ROE contact of both 2‘- and 3‘-OH with water. The presence of a hydrophilic 3‘-phosphate group in 1 causes a much higher water activity in the vicinity of its 2‘-OH, which in turn causes the 2‘-OH to exchange faster, culminating in a shorter exchange lifetime (τ) for 2‘-OH proton with HOD in 1 (τ2‘-OH:  489 ms) compared to that in 3 (τ2‘-OH:  6897 ms). The activation energy (Ea) of the exchange with the bound-water for 2‘- and 3‘-OH in 3 (48.3 and 45.0 kJ mol-1, respectively) is higher compared to that of 2‘-OH in 1 (31.9 kJ mol-1), thereby showing that the kinetic availability of hydrated 2‘-OH in 1 for any inter- and intramolecular interactions, in general, is owing to the vicinal 3‘-phosphate residue. It also suggests that 2‘-OH in native RNA can mediate other inter- or intramolecular interactions only in competition with the bound-water, depending upon the specific chemical nature and spatial orientation of other functions with potential for hydrogen bonding in the neighborhood. This availability of the bound water around 2‘-OH in RNA would, however, be dictated by whether the vicinal phosphate is exposed to the bulk water or not. This implies that relatively poor hydration around a specific 2‘-OH across a polyribonucleotide chain, owing to some hydrophobic microenvironmental pocket around that hydroxyl, may make it more accessible to interact with other donor or acceptor functions for H-bonding interactions, which might then cause the RNA to fold in a specific manner generating a new motif leading to specific recognition and function. Alternatively, a differential hydration of a specific 2‘-OH may modulate its nucleophilicity to undergo stereospecific transesterification reaction as encountered in ubiquitous splicing of pre-mRNA to processed RNA or RNA catalysis, in general.

Item Type: Article
Uncontrolled Keywords: hydrogen bonding, nucleic acid, hydration, NMR, Ab initio, molecular modeling
Subjects: Q Science > Q Science (General)
Faculty / Department / Research Group: Faculty of Engineering & Science
Faculty of Engineering & Science > Natural Resources Institute
Faculty of Engineering & Science > Natural Resources Institute > Food & Markets Department
Last Modified: 08 Jul 2020 13:48
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
Selected for REF2021: None

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