Biochemical characterization of the kink-turn RNA motif

RNA, which acts as a medium for transmitting genetic information, plays a variety of roles in a cell. As with proteins, elucidation of the three- dimensional (3D) structures of RNAs is important for understanding their various roles. Determination of the atomic structures of crystallized ribosome has enabled the identification of previously unknown RNA structural motifs. The kink-turn (K-turn or GA) motif, which causes a sharp bend in an RNA double helix, was identified as one of these structural motifs. To biochemically characterize the K-turn, the motif was inserted into a hinge region of P4-P6 RNA, which is the most extensively studied self-folding RNA, and its properties were investigated. The stability and metal ion requirement of the constructs containing three different K-turn motifs were analyzed using native PAGE and dimethyl sulfate (DMS) modification. The formation of the sharp bending structure depends on the presence of divalent cation like Mg2+ or Ca2+, although its required concentration is different for each motif.