Twist-joints and double twist-joints in RNA structure.

Analysis of available RNA crystal structures has allowed us to identify a new family of RNA arrangements that we call double twist-joints, or DTJs. Each DTJ is composed of a double helix that contains two bulges incorporated into different strands and separated from each other by 2 or 3 bp. At each bulge, the double helix is over-twisted, while the unpaired nucleotides of both bulges form a complex network of stacking and hydrogen-bonding with nucleotides of helical regions. In total, we identified 14 DTJ cases, which can be combined in three groups based on common structural characteristics. One DTJ is found in a functional center of the ribosome, another DTJ mediates binding of the pre-tRNA to the RNase P, and two more DTJs form the sensing domains in the glycine riboswitch.