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

Although RNA interactions with K+ and Mg2+ have been studied extensively, much less is known about the third most abundant cation in bacterial cells, putrescine2+, and how RNA folding might be influenced by the three ions in combination. In a new approach, we have observed the competition between Mg2+ and putrescine2+ (in a background of K+) with native, partially unfolded and highly extended conformations of an adenine riboswitch aptamer. With the native state, putrescine2+ is a weak competitor when the ratio of the excess Mg2+ (which neutralizes phosphate charge) to RNA is very low, but becomes much more effective at replacing Mg2+ as the excess Mg2+ in the RNA ion atmosphere increases. Putrescine2+ is even more effective in competing Mg2+ from the extended conformation, independent of the Mg2+ 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 Mg2+. The sensitivity of RNA folding to the combination of Mg2+ and putrescine2+ found in vivo depends on the architectures of both the unfolded and native conformations.