Riboswitches are highly structured mRNA elements that regulate gene expression upon specific binding of small metabolite molecules. The purine-binding riboswitches bind different purine ligands by forming both canonical Watson—Crick and non-canonical intermolecular
base pairs, involving a variety of hydrogen bonds between the riboswitch aptamer domain and the purine ligand. Here, we summarize
work on the ligand binding modes of both purine-binding aptamer domains, their con-formational characteristics in the free
and ligand-bound forms, and their ligand-induced folding. The adenine- and guanine-binding riboswitch aptamer domains display
different conformations in their free forms, despite nearly identical nucleotide loop sequences that form a loop—loop interaction
in the ligand-bound forms. Interestingly, the stability of helix II is crucial for the formation of the loop—loop interaction
in the free form. A more stable helix II in the guanine riboswitch leads to a preformed loop—loop interaction in its free
form. In contrast, a less stable helix II in the adenine riboswitch results in a lack of this loop—loop interaction in the
absence of ligand and divalent cations.
| 