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Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction

Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction

Acharya, P. ORCID: 0000-0003-2521-9968, Acharya, S. and Foldesi, A. (2003) Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction. Journal of the American Chemical Society, 125 (8). pp. 2094-2100. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja028277h)

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Abstract

We here show an electrostatic polar-π interaction from the first to the third aglycon, via the second aglycon, in the ground state in two single stranded trimeric RNAs, 5‘-GpA1pA2-3‘ (3) and 5‘-GpApC-3‘ (4), as a result of intramolecular nearest neighbor offset-stacking. The experimental evidence in support of this conclusion has been obtained by comparing the pKas of each aglycone in the two trimers with those of guanosine 3‘-ethyl phosphate, GpEt (1) and 5‘-GpA-3‘ (2):  Thus, the pKa of N1-H of guanin-9-yl of 5‘-GpA1pA2-3‘ (3) could be measured by pH titration (pH 7.3−11.6) of its own δH8G (pKa 9.75 ± 0.02) as well as from δH8A1 (pKa 9.72 ± 0.02) and δH2A1 (pKa 9.83 ± 0.04) of the neighboring pA1p moiety and the δH8A2 (pKa 9.83 ± 0.02) of the terminal pA2 moiety. Similarly, the pH titration of GpApC (4) shows the pKa of N1-H of guanin-9-yl from its own δH8G (pKa 9.88 ± 0.03) as well as from δH8A (pKa 9.87 ± 0.01) of the neighboring pAp moiety, and δH5/H6C (pKa 9.88 ± 0.01 and 9.90 ± 0.01 respectively) of the 3‘-terminal cytosin-1-yl. This intramolecular nearest neighbor electrostatic interaction in the single-stranded RNA modulates the pseudoaromaticity of the nearest neighbors by almost total transmission of because they constitute an extended array of offset-stacked coupled aromatic heterocycles within a polyanionic sugar−phosphate backbone at the ground state. The enhanced basicity of Gp residue by ca. 0.6 pKa unit in the trimers compared to that of the dimer is a result of the change in the electrostatic microenvironment owing to the nearest neighbors in the former (the nucleobases as well as the phosphates). Thus, the from the 5‘-guanylate ion to the 3‘-end aglycon via the central adenin-9-yl is 55 to 56 kJ mol-1 in each step through a distance spanning ∼6.8 Å in an unfolded state. As a result, the pKa of guanin-9-yl moiety has become 9.25 ± 0.02 in GpEt (1), 9.17 ± 0.02 in GpA (2), 9.75 ± 0.02 in GpApA (3), and 9.88 ± 0.03 in GpApC (4). This means that guanin-9-yl moiety of trimers 3 and 4 is more basic than in the monomer or the dimer. The net outcome of this electrostatic cross-talk between the two neighboring heterocycles is creation of new hybrid aglycones in an oligo or polynucleotide, whose physicochemical property and the pseudoaromatic character are completely dependent both upon the nearest neighbors, and whether they are stacked or unstacked. Thus, this tunable physicochemical property of an aglycon (an array of the extended genetic code) may have considerable implication in our understanding of the specific ligand binding ability of an aptamer, the pKa and the hydrogen bonding ability of nucleic acids in a microenvironment, or in the triplet usage by the anticodon−codon interaction in the protein biosynthesis in the ribosome.

Item Type: Article
Uncontrolled Keywords: nucleobase, genetics, molecular interaction
Subjects: Q Science > QD Chemistry
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: 10 Jul 2020 13:34
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
Selected for REF2021: None
URI: http://gala.gre.ac.uk/id/eprint/28726

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