Helix-turn-helix motif

Helix-turn-helix motif (DNA) is a part located on DNA being transcribed that need to be recognized specific proteins such as trp repressor and CAP. This structure binds to the protein. It consists of two alpha helices link by a short nonhelical segment of amino acids (the turn). One helix is the recognition helix which contains an R group sticking out, it binds the DNA in the Minor groove by interacting with the nitrogenous base. The recognition helix is the major factor, in the DNA sequence, which helps binding. The other helix is the stabilization helix. It usually lies right across from the recognition helix and helps the recognition helix lie down into the groove. It helps increase the attraction of binding only contributes a little bit to the specificity of the DNA sequence.