Slight sequence modifications unexpectedly alter the metal-dependency of a kissing-loop interaction.

Abstract

Kissing-loop RNA-RNA interactions play essential roles in many biological processes. Here, by a modified SELEX (Systematic Evolution of Ligands by EXponential enrichment) procedure, we obtained a new kissing-loop RNA motif that binds the HIV-1 transactivation responsible (TAR) RNA. Surface plasmon resonance (SPR) analyses of this RNA motif, as well as similar RNA motifs previously reported, showed unexpected differences for divalent cation dependency. This result emphasizes the complex roles for metal ions even on simple RNA structures.