Electrostatic cross-modulation of the pseudoaromatic character in single-stranded RNA by nearest-neighbor interactions

Abstract

The generation of a single anionic or cationic center at an alkaline or acidic pH in a given molecule presents a unique opportunity to examine the electrostatic make-up of these molecules both at the neutral or ionic state. The generation of a single cationic center in the phenyl-nicotinamide system provided new straightforward evidence showing that the charge density of the electron-deficient pyridinium was actually enhanced by the donation of the charge from the electron-rich phenyl group (i.e., the pyridinyl became more basic by ca. 0.5 pK_a unit compared to an analogous system where phenyl was absent) owing to the electrostatic interactions between these two moieties. On the other hand, the generation of the 5'-guanylate ion in the hexameric single-strand (ss) RNA [5'-GAAAAC-3'], in comparison with the constituent trimeric, tetrameric, and pentameric-ssRNAs, has unequivocally shown how far the electrostatic cross-talk (as an interplay of Coulombic attractive or repulsive forces) in this electronically coupled system propagates through the intervening pAp nucleotide steps until the terminal pC-3' residue in comparison with the neutral counterpart. The footprint of the propagation of this electrostatic cross-talk among the neighboring nucleobases is evident by measurement of pK_as from the marker protons of ionization point (i.e., of G) as well as from the neighboring marker protons (i.e., of A or C) in the vicinity, as well as from the change of the chemical environment (i.e., chemical shifts) around their aromatic marker protons (δH2, δH8, δH5, and δH6) owing to a change of the stacking-destacking equilibrium as a function of pH.