Comparison of interactions of diamine and Mg²âº with RNA tertiary structures: similar versus differential effects on the stabilities of diverse RNA folds.

ABSTRACT

Cations play a large role in stabilizing the native state of RNA in vivo. In addition to Mg²âº, putrescine²âº is an abundant divalent cation in bacterial cells, but its effect on the folding of RNA tertiary structure has not been widely explored. In this study, we look at how the stabilities of four structured RNAs, each with a different degree of dependence on K⁺ and Mg²âº, are affected by putrescine²âº relative to Mg²âº. Through the use of thermal melts, we observe that (i) at a given concentration, putrescine²âº is less effective than Mg²âº at stabilizing RNA, (ii) the stability imparted to RNA by various diamines is a function of charge density (average separation distance between charges) as well as the flexibility of the counterion, and (iii) when Mg²âº is already present in a buffer, further addition of putrescine²âº may either destabilize or stabilize RNA structure, depending on whether the native RNA does or does not chelate Mg²âº ion, respectively. At ion concentrations likely to be found in vivo, the effect of putrescine²âº on the free energy of folding of an RNA tertiary structure is probably quite small compared to that of Mg²âº, but the ability of mixed Mg²âº/putrescine²âº environments to (in effect) discriminate between different RNA architectures suggests that, in some cells, the evolution of functional RNA structures may have been influenced by the presence of putrescine²âº.