Publication – Schwalbe, Wöhnert

Mechanisms for differentiation between cognate and near-cognate ligands by purine riboswitches.

Wacker A, Buck J, Richter C, Schwalbe H, Wöhnert J. RNA Biol, 2012 May 1. Abstract or full publication here.

Riboswitches are elements in the 5′-untranslated region of mRNAs that regulate gene expression by directly interacting with metabolites related to their own gene products. A remarkable feature of this gene regulation mechanism is the high specificity of riboswitches for their cognate ligands. In this study, we used a combination of static and time-resolved NMR-spectroscopic methods to investigate the mechanisms for ligand specificity in purine riboswitches. We investigate the xpt-aptamer domain from a guanine-responsive riboswitch and the mfl-aptamer domain from a 2′-deoxyguanosine-responsive riboswitch. The xpt-aptamer binds the purine nucleobases guanine/hypoxanthine with high affinity, but, unexpectedly, also the nucleoside 2′-deoxyguanosine. On the other hand, the mfl-aptamer is highly specific for its cognate ligand 2′-deoxyguanosine, and does not bind purine ligands. We addressed the question of aptamer`s ligand specificity by real-time NMR spectroscopy. Our studies of ligand binding and subsequently induced aptamer folding revealed that the xpt-aptamer discriminates against non-cognate ligands by enhanced life-times of the cognate complex compared with non-cognate complexes, whereas the mfl-aptamer rejects non-cognate ligands at the level of ligand association, employing a kinetic proofreading mechanism.