Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3‘→5‘) Monophosphates by the Nearest Neighbor Interaction in the Stacked State

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Abstract
Each nucleobase in a series of stacked dinucleoside (3‘→5‘) monophosphates, in both acidic and alkaline pH, shows (1H NMR) not only its own pKa but also the pKa of the neighboring nucleobase as a result of cross-modulation of two-coupled π systems of neighboring aglycones. This means that the electronic character of two nearest neighbors are not like the monomeric counterparts anymore; they have simultaneously changed, almost quantitatively, to something that is a hybrid of the two due to two-way transmission of charge (i.e. 3‘→5‘ as well as 5‘→3‘). This change is permanent due to total modulation of each others pseudoaromatic character by intramolecular stacking, which can be tuned by the nature of the medium across the whole pH range. The small difference observed in the pKa of the dimer compared to the monomer is a result of the change in microenvironment in the former. The charge transfer takes place between two stacked nucleobases from the negatively charged end because of the attempt to minimize the charge difference between the two neighboring pseudoaromatic aglycones. Experimental evidence points that the charge transmission in the stacked state takes place by atom−πσ interaction between nearest neighbor nucleobases in 1−6. The net result of this cross-talk between two neighboring aglycones is a unique set of aglycones in an oligo- or polynucleotide, whose physicochemical property and the pseudoaromatic character are completely dependent both upon the sequence makeup, and whether they are stacked or unstacked. Thus, the physicochemical property of individual nucleobases in an oligonucleotide is determined in a tunable manner, depending upon who the nearest neighbors are, which may have considerable implication in the specific ligand binding ability of an aptamer, the pKa and the hydrogen bonding ability in a microenvironment, in the use of codon triplets in the protein biosynthesis or in the triplet usage by the anticodon−codon interaction.

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