Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding

Although RNA interactions with K(+) and Mg(2+) have been studied extensively, much less is known about the third most abundant cation in bacterial cells, putrescine(2+), and how RNA folding might be influenced by the three ions in combination. In a new approach, we have observed the competition between Mg(2+) and putrescine(2+) (in a background of K(+)) with native, partially unfolded and highly extended conformations of an adenine riboswitch aptamer. With the native state, putrescine(2+) is a weak competitor when the ratio of the excess Mg(2+) (which neutralizes phosphate charge) to RNA is very low, but becomes much more effective at replacing Mg(2+) as the excess Mg(2+) in the RNA ion atmosphere increases. Putrescine(2+) is even more effective in competing Mg(2+) from the extended conformation, independent of the Mg(2+) excess. To account for these and other results, we propose that both ions closely approach the surface of RNA secondary structure, but the completely folded RNA tertiary structure develops small pockets of very negative electrostatic potential that are more accessible to the compact charge of Mg(2+). The sensitivity of RNA folding to the combination of Mg(2+) and putrescine(2+) found in vivo depends on the architectures of both the unfolded and native conformations.